Nanomaterial-Assisted Signal Enhancement of Hybridization for DNA Biosensors: A Review
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paper_title: Generalizations for the Potential of Mean Force between Two Isolated Colloidal Particles from Monte Carlo Simulations

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A substantial amount of experimental and numerical evidence has shown that the Derjaguin–Landau–Verwey–Overbeek theory is not suitable for describing those colloidal solutions that contain multivalent counterions. Toward improved understanding of such solutions, the authors report Monte Carlo calculations wherein, following Rouzina and Bloomfield, they postulate that, in the absence of van der Waals forces, the overall force between two isolated charged colloidal particles in electrolyte solutions is determined by a dimensionless parameter Γ=z2lB/a, which measures the electrostatic repulsion between counterions adsorbed on the macroion surface, where z = counterion valence, lB=Bjerrum length, and a = average separation between counterions on the macroion surface calculated as if the macroion were fully neutralized. The authors find, first, that the maximum repulsion between like-charged macroions occurs at Γ≈0.5 and, second, that onset of attraction occurs at Γ≈1.8, essentially independent of the valence and concentration of the surrounding electrolyte. These observations might provide new understanding of interactions between electrostatic double layers and perhaps offer explanations for some electrostatic phenomena related to interactions between DNA molecules or proteins.
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paper_title: Ultrasensitive DNA sequence detection using nanoscale ZnO sensor arrays

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We report that engineered nanoscale zinc oxide structures can be effectively used for the identification of the biothreat agent, Bacillus anthracis by successfully discriminating its DNA sequence from other genetically related species. We explore both covalent and non-covalent linking schemes in order to couple probe DNA strands to the zinc oxide nanostructures. Hybridization reactions are performed with various concentrations of target DNA strands whose sequence is unique to Bacillus anthracis. The use of zinc oxide nanomaterials greatly enhances the fluorescence signal collected after carrying out duplex formation reaction. Specifically, the covalent strategy allows detection of the target species at sample concentrations at a level as low as a few femtomolar as compared to the detection sensitivity in the tens of nanomolar range when using the non-covalent scheme. The presence of the underlying zinc oxide nanomaterials is critical in achieving increased fluorescence detection of hybridized DNA and, therefore, accomplishing rapid and extremely sensitive identification of the biothreat agent. We also demonstrate the easy integration potential of nanoscale zinc oxide into high density arrays by using various types of zinc oxide sensor prototypes in the DNA sequence detection. When combined with conventional automatic sample handling apparatus and computerized fluorescence detection equipment, our approach can greatly promote the use of zinc oxide nanomaterials as signal enhancing platforms for rapid, multiplexed, high-throughput, highly sensitive, DNA sensor arrays.
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paper_title: Arabidopsis thaliana Full Genome Longmer Microarrays: A Powerful Gene Discovery Tool for Agriculture and Forestry

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Sequenced plant genomes provide a large reservoir of known genes with potential for use in crop and tree improvement, but assignment of specific functions to annotated genes in sequenced plant genomes remains a challenge. Furthermore, most plant genes belong to families encoding proteins with related but distinct functions. In this commentary, we discuss our development of Arabidopsis spotted whole genome longmer oligonucleotide microarrays, and their use in global transcription profiling. We show that longmer array based transcriptome analysis in Arabidopsis can be used as an efficient and effective gene discovery and functional genomics tool, particularly for functional analyses of members of large gene families. We discuss experiments that focus on gene families involved in phenylpropanoid natural product biosynthesis and fiber differentiation. These analyses have helped to elucidate functions of individual gene family members, and have identified new candidate genes involved in fiber development and differentiation. Results obtained by these studies in Arabidopsis can be used as the basis for gene discovery in commercially important plants, and we have focused our attention on Populus trichocarpa (poplar), a species important in forestry and agroforestry for which complete genome sequence information is available.
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paper_title: Gold Nanoparticle-Based Redox Signal Enhancement for Sensitive Detection of Human Chorionic Gonadotropin Hormone

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A sensitive immunosensor for the detection of pregnancy marker, human chorionic gonadotropin hormone (hCG), was developed using the direct electrical detection of Au nanoparticles. We utilized disposable screen-printed carbon strips (SPCSs) for the development of our immunosensor, which provided cost-effective tests with the required antigen sample volume as small as 2 μL. After the recognition reaction between the surface-immobilized primary antibody and hCG, the captured antigen was sandwiched with a secondary antibody that was labeled with Au nanoparticles. Au nanoparticles were exposed to a preoxidation process at 1.2 V for 40 s, which was subsequently followed with a reduction scan on the same surface using differential pulse voltammetry (DPV). We could observe Au nanoparticle-labeled antigen-antibody complexes immobilized on the surface of SPCS using scanning electron microscopy (SEM). Additionally, the number of Au nanoparticles on the immunosensor was determined using SEM images, and showed a linear relationship with the current intensity obtained from the DPV measurements with a detection limit of 36 pg/mL hCG (612 fM, 3.6×10−4 IU/mL). Our immunosensor system, a combination of the screen-printing technology with Au nanoparticles provides a promising biosensor for various applications in life sciences.
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paper_title: UHRF1 Plays a Role in Maintaining DNA Methylation in Mammalian Cells

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Epigenetic inheritance in mammals relies in part on robust propagation of DNA methylation patterns throughout development. We show that the protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1), also known as NP95 in mouse and ICBP90 in human, is required for maintaining DNA methylation. UHRF1 colocalizes with the maintenance DNA methyltransferase protein DNMT1 throughout S phase. UHRF1 appears to tether DNMT1 to chromatin through its direct interaction with DNMT1. Furthermore UHRF1 contains a methyl DNA binding domain, the SRA (SET and RING associated) domain, that shows strong preferential binding to hemimethylated CG sites, the physiological substrate for DNMT1. These data suggest that UHRF1 may help recruit DNMT1 to hemimethylated DNA to facilitate faithful maintenance of DNA methylation.
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paper_title: Control of Surface Plasmon Localization via Self-Assembly of Silver Nanoparticles along Silver Nanowires

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A simple and low-cost method to create metal-metal hybrid nanostructures possessing fairly regularly spaced "hot-spots" of surface plasmon resonances is proposed. The nanohybrid structure was prepared via self-assembly during a simple drop-casting procedure, using chemically synthesized silver nanowires and silver nanoparticles prepared in a single batch of a polyol process. Wide field illumination of these nanohybrids produced hot-spots with spacings of around 500 nm to 1 microm. The intensity of the emission/scattering from the hot-spots fluctuates over time. The proposed structure can be useful for the development of molecular-sensors or as a substrate for surface enhanced Raman/fluorescence spectroscopy.
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paper_title: Microarray analysis in drug discovery and clinical applications.

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DNA microarray analyzes genome-wide gene expression patterns and is used in many areas including drug discovery and clinical applications. This chapter summarizes some of these applications such as identification and validation of anti-infective drug target, study mechanisms of drug action and drug metabolism, classification of different types of tumors, and use of molecular signatures for prediction of disease outcome. A step-by-step protocol is provided for sample preparation, sample labeling and purification, hybridization and washing, feature extraction, and data analysis. Important considerations for a successful experiment are also discussed with emphasis on drug discovery and clinical applications. Finally, a clinical study is presented as an example to illustrate how DNA microarray technology can be used to identify gene signatures, and to demonstrate the promise of DNA microarray as a clinical tool.
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paper_title: Synthesis, Electronic Structure, and Raman Scattering of Phosphorus-Doped Single-Wall Carbon Nanotubes

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Substitutional phosphorus doping in single-wall carbon nanotubes (SWNTs) is investigated by density functional theory and resonance Raman spectroscopy. Electronic structure calculations predict charge localization on the phosphorus atom, generating nondispersive valence and conduction bands close to the Fermi level. Besides confirming sustitutional doping, accurate analysis of electron and phonon renormalization effects in the double-resonance Raman process elucidates the different nature of the phosphorus donor doping (localized) when compared to nitrogen substitutional doping (nonlocalized) in SWNTs.
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paper_title: In situ QCM DNA-biosensor probe modification

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We report on a probe modification of a quartz crystal microbalance (QCM) DNA-biosensor that permits to reversibly change the DNA sequence detected. A QCM DNA-biosensor was designed by immobilization of a 20-base DNA-disulfide probe on the gold-covered quartz surface of a 27 MHz microbalance (9 MHz, third overtone). After immobilization on the gold covered quartz surface, this probe was modified by hybridization with a 45-base DNA that includes the complementary 20-base sequence, a 5-base spacer and a non-complementary 20-base sequence. The non-complementary sequence constitutes a new probe, different from the DNA-disulfide probe, that permits the detection of a new DNA target. As this 45 bases DNA is changeable by dehybridization, successive different DNA targets can be detected. Kinetics and thermodynamic studies of the DNA-disulfide and modified biosensors indicate that the modified biosensor is as sensitive, selective, fast, renewable and reproducible as the DNA-disulfide biosensor, but with a higher hybridization ratio. This modification method offers wider investigation field and practical and economic advantages to DNA-biosensors based on irreversible immobilization of DNA probes on solid substrate.
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paper_title: Low-temperature sensing and high sensitivity of ZnO nanoneedles due to small size effect

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ZnO nanoneedles were synthesized through a simple wet chemical route at room temperature. The diameters of the ZnO nanoneedles tips and roots are about 5 nm and 10 nm, respectively. The sensors fabricated by ZnO nanoneedles exhibited good sensing properties. The sensitivity is 173 against 100 ppm ethanol and the working temperature can be lowered to 150 °C. Additionally, a linear dependence of the sensitivity on the ethanol concentration was also observed. These excellent sensing properties can be ascribed to the small size effects, which can be further confirmed by the calculated results.
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paper_title: Geometrical enhancement of the proximity effect in quantum wires with extended superconducting tunnel contacts

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We study Andreev reflection in a ballistic one- dimensional channel coupled in parallel to a superconductor via a tunnel barrier of finite length {\it L}. The dependence of the low-energy Andreev reflection probability {\it R$_{A}$} on {\it L} reveals the existence of a characteristic length scale {\it $\xi$;$_{N}$} beyond which {\it R$_{A}$(L)} is enhanced up to unity despite the low interfacial transparency. The Andreev reflection enhancement is due to the strong mixing of particle and hole states that builds up in contacts exceeding the coherence length {\it $\xi$;$_{N}$}, leading to a small energy gap (minigap) in the density of states of the normal system. The role of the geometry of such hybrid contacts is discussed in the context of the experimental observation of zero-bias Andreev anomalies in the resistance of extended carbon nanotube/superconductor junctions in field effect transistor setups.
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paper_title: Enhanced surface plasmon resonance imaging detection of DNA hybridization on periodic gold nanoposts

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We explore periodic gold nanoposts as substrates for the enhanced surface plasmon resonance imaging (SPRi) detection of DNA hybridization. Rigorous coupled-wave analysis was used to model and design the nanopost-based SPRi biosensor. Arrayed gold nanoposts on gold-coated glass substrate, with various widths and periodicity, were fabricated using electron-beam lithography and characterized with scanning electron and atomic force microscopy. A scanning-angle SPRi apparatus was used to conduct the kinetic analysis of DNA hybridization on nanopost-based sensor surface and assess the corresponding SPR signal amplification. Experimental results showed that both the nanostructure size and period influenced the SPR signal enhancement; the optimized 30 nm height, 50 nm size, and 110 nm period nanoposts provided a fivefold SPR signal amplification compared with the plain 50 nm thick gold film used as control.
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paper_title: Nucleic Acid Conjugated Nanomaterials for Enhanced Molecular Recognition

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Nucleic acids, whether designed or selected in vitro, play important roles in biosensing, medical diagnostics, and therapy. Specifically, the conjugation of functional nucleic acid based probe molecules and nanomaterials has resulted in an unprecedented improvement in the field of molecular recognition. With their unique physical and chemical properties, nanomaterials facilitate the sensing process and amplify the signal of recognition events. Thus, the coupling of nucleic acids with various nanomaterials opens up a promising future for molecular recognition. The literature offers a broad spectrum of recent advances in biosensing by employing different nanoplatforms with designed nucleic acids, especially gold nanoparticles, carbon nanotubes, silica nanoparticles, and quantum dots. The advantages of these novel combinations are discussed from the perspective of molecular recognition in chemistry, biology, and medicine, along with the problems confronting future applications.
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paper_title: Dimers of silver nanospheres: facile synthesis and their use as hot spots for surface-enhanced Raman scattering.

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This paper describes a simple, one-pot method that generates dimers of silver nanospheres in one step without any additional assembly steps. The dimers are consisted of single-crystal silver nanospheres ∼30 nm in diameter and separated by a gap of 1.8 nm wide. The key to the success of this method lies in the control of colloidal stability and oxidative etching by optimizing the amount of chloride added to a polyol synthesis. The dimers provide a well-defined system for studying the hot spot phenomenon (hot spot: the gap region of a pair of strongly coupled silver or gold nanoparticles), an extremely important but poorly understood subject in surface-enhanced Raman scattering (SERS). Because of the relatively small size of the silver nanospheres, only those molecules trapped in the hot spot region are expected to contribute to the detected SERS signals. By correlating SERS measurements with SEM imaging, we found that the SERS enhancement factor within the hot spot region of such a dimer was on the order o...
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paper_title: Discovering genes are made of DNA

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Maclyn McCarty is the sole surviving member of the team that made the remarkable discovery that DNA is the material of inheritance. This preceded by a decade the discovery of the structure of DNA itself. Here he shares his personal perspective of those times and the impact of the double helix. Editor's note — For a long time, biologists thought that 'genes', the units of inheritance, were made up of protein. In 1944, in what was arguably the defining moment for nucleic acid research, Oswald Avery, Maclyn McCarty and Colin MacLeod, at Rockefeller Institute (now University) Hospital, New York, proved that DNA was the material of inheritance, the so-called stuff of life. They showed that the heritable property of virulence from one infectious strain of pneumococcus (the bacterial agent of pneumonia) could be transferred to a noninfectious bacterium with pure DNA1. They further supported their conclusions by showing that this 'transforming' activity could be destroyed by the DNA-digesting enzyme DNAase2,3. This work first linked genetic information with DNA and provided the historical platform of modern genetics. Their discovery was greeted initially with scepticism, however, in part because many scientists believed that DNA was too simple a molecule to be the genetic material. And the fact that McCarty, Avery and MacLeod were not awarded the Nobel prize is an oversight that, to this day, still puzzles.
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paper_title: Impact of quantum confinement and quantum confined Stark effect on biexciton binding energy in GaN/AlGaN quantum wells

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We report on time-resolved photoluminescence measurements carried out along the thickness gradient of two types of GaN∕AlGaN quantum wells with low Al content in the barriers (5% and 9%, respectively). A reduction of the biexciton binding energy with increasing well thickness is observed, as a result of the reduced quantum confinement and the increasing impact of the quantum confined Stark effect. In the sample with 5% Al content in the barriers, for thicknesses of the well region larger than ∼9 monolayers, the biexciton binding energy is found to be smaller than that measured for bulk GaN.
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paper_title: Fast DNA Sequencing via Transverse Electronic Transport

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A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, that is, orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict, and cure diseases from the perspective of the genetic makeup of each individual.
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paper_title: Nanopore-based single-molecule DNA analysis

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Nanopore-based DNA analysis is a single-molecule technique with revolutionary potential. It promises to carry out a range of analyses, orders of magnitude faster than current methods, including length measurement, specific sequence detection, single-molecule dynamics and even de novo sequencing. The concept involves using an applied voltage to drive DNA molecules through a narrow pore that separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the pore, they block the flow of ions and, thus, their structure and length can be determined based on the degree and duration of the resulting current reductions. In this review, I explain the nanopore-based DNA analysis concept and briefly explore its historical foundations, before discussing and summarizing all experimental results reported to date. I conclude with a summary of the obstacles that must be overcome for it to realize its promised p...
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paper_title: Functional DNA directed assembly of nanomaterials for biosensing

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This review summarizes recent progress in the development of biosensors by integrating functional DNA molecules with different types of nanomaterials, including metallic nanoparticles, semiconductor nanoparticles, magnetic nanoparticles, and carbon nanotubes. On one hand, advances in nanoscale science and technology have generated nanomaterials with unique optical, electrical, magnetic and catalytic properties. On the other hand, recent progress in biology has resulted in functional DNAs, a new class of DNAs that can either bind to a target molecule (known as aptamers) or perform catalytic reactions (known as DNAzymes) with the ability to recognize a broad range of targets from metal ions to organic molecules, proteins and cells specifically. By taking advantage of the strengths in both fields, the physical and chemical properties of nanomaterials have been modulated by the target recognition and catalytic activity of functional DNAs in the presence of a target analyte, resulting in a large number of colorimetric, fluorescent, electrochemical, surface-enhanced Raman scattering and magnetic resonance imaging sensors for the detection of a broad range of analytes with high sensitivity and selectivity.
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paper_title: Direct Evidence for the Effect of Quantum Confinement of Surface-State Electrons on Atomic Diffusion

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We report on the direct observations of the effect of quantum confinement of surface-state electrons on atomic diffusion. Confined electronic states induced by open nanoscale resonators [consisting of two parallel monatomic Cu chains on Cu(111)] are studied by means of scanning tunneling microscope measurements and first-principles calculations. Strongly anisotropic diffusion of adatoms around and inside resonators is revealed at low temperatures. The formation of diffusion channels and empty zones is demonstrated. We show that it is possible to engineer atomic diffusion by varying the distance between the resonator walls.
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paper_title: Disasters drive DNA forensics to reunite families

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Genetics innovations may help Holocaust survivors.
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paper_title: The formation of TiO(2) nanowires directly from nanoparticles.

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TiO2 nanowires were fabricated by annealing TiO2 nanoparticles on silicon substrate at 1000 °C in air. When a polystyrene nanosphere monolayer was used as a template to separate the TiO2 nanoparticles, they could more easily react with the silicon substrate to form Ti5Si3. The TiO2 nanowires were formed upon further oxidation of Ti5Si3. The diameters and lengths of TiO2 nanowires were 30–80 nm and 1–3 µm, respectively. The nanowires had a rutile structure with the growth direction [112]. It is believed that the formation of TiO2 nanowires involved a precipitation process in the mixture of SiO2 and TiO2. The nanowires show different photoluminescence behavior from that of the powder.
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paper_title: Nanomaterials and chip-based nanostructures for capillary electrophoretic separations of DNA

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Capillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip-based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip-based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low-viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.
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paper_title: DNA oligonucleotide-assisted genetic manipulation increases transformation and homologous recombination efficiencies: Evidence from gene targeting of Dictyostelium discoideum

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Artificial gene alteration by homologous recombination in living cells, termed gene targeting, presents fundamental and considerable knowledge of in vivo gene function. In principle, this method can possibly be applied to any type of genes and transformable cells. However, its success is limited due to a low frequency of homologous recombination between endogenous targeted gene and exogenous transgene. Here, we describe a general gene-targeting method in which co-transformation of DNA oligonucleotides (oligomers) could significantly increase the homologous recombination frequency and transformation efficiency. The oligomers were simply designed such that they were identical to both the ends of the homologous flanking regions of the targeting construct. Using this strategy, both targeted alleles of diploid cells were simultaneously replaced in a single transformation procedure. Thus, the simplicity and versatility of this method applicable to any type of cell may increase the application of gene targeting.
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paper_title: Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta.

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DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to gain resistance against cisplatin-based chemotherapy. It allows cells to replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG) and UV-induced cis-syn thymine dimers. We present structural and biochemical analysis of how Pol eta copies Pt-GG-containing DNA. The damaged DNA is bound in an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an active conformation, driven by hydrogen bonding of the templating base to the dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick base pair to dCTP and is biochemically efficient and accurate. In contrast, bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and dATP as a result of the presence of the rigid Pt cross-link. Our analysis reveals the set of structural features that enable Pol eta to replicate across strongly distorting DNA lesions.
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paper_title: Gold/Iron Oxide Core/Hollow‐Shell Nanoparticles

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Assembling several materials into a single nanoparticle (NP) is an attractive way to design systems possessing diverse physical and chemical properties. In multicomponent systems, one can expect novel and unique properties that originate from collective interactions between the constituents. Multicomponent nanoparticles exhibit distinct optical, catalytic, and photocatalytic properties. To date, several morphologies of multicomponent nanoparticles have been reported. The general strategy to synthesize multicomponent materials is first to prepare nanoparticles of one material, and then use them as nucleation seeds to deposit the other components. Significant progress has been made in the synthesis of semiconductor nanoparticles with epitaxial shells, while the synthesis of nanoparticles that combine components with very different lattice parameters still faces many challenges. To date, a number of heterostructures have been successfully synthesized through seed-mediated approaches. However, only a few hybrid nanoparticles show a reasonable level of control over particle size distribution and homogeneity in composition. It was recently shown that CoPt3/Au dumbbells, [2] PbSe/Aux heterostructures, Au/Fe3O4 dumbbells and solid core/shell structures, [5] anisotropic Fe2O3 nanoparticles decorated with a polycrystalline Au shell, and Pt/CoO core/hollow-shell nanoparticles can be obtained at the nanoscale. Iron oxide based
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paper_title: Genetic diversity and individual identification of reintroduced otters (Lutra lutra) in north-eastern Spain by DNA genotyping of spraints

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During the last century, otter populations in the Mediterranean area of the Iberian Peninsula were dramatically reduced and disappeared in many localities. A reintroduction programme was established in north-eastern Spain (Muga and Fluvia basins and the “Aiguamolls de l’Emporda” wetlands), by releasing 42 otters from four different Iberian populations, between 1995 and 2002. In order to evaluate the success of the reintroduction programme, we investigated microsatellite variation in the native populations of released otters as well as in the population present in the release area in 2004. We used non-invasively collected samples as the DNA source to avoid disturbing the animals in the wild. Laboratory procedures included the screening of samples and a multiple-tubes approach to detect and correct genotyping errors. Our results show that founders have been replaced by descendants in the release area and the population is in Hardy-Weinberg equilibrium, with a 1:1 sex ratio. Western Iberian otters—representing two-thirds of the founder group and released earlier—have greatly contributed to the genetic composition of the current population. The genetic patterns of otters found in a basin north of the studied area suggest a common origin with the released population. We also detected in a few otters the presence of alleles not identified in the original founder group, and we shall discuss the possible origin of these alleles.
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paper_title: Self-assembly of Mn-doped ZnS quantum dots/octa(3-aminopropyl)octasilsequioxane octahydrochloride nanohybrids for optosensing DNA.

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Simple plan! Nanohybrids have been built from capped Mn-doped ZnS quantum dots and octa(3-aminopropyl)octasilsequioxane octahydrochloride (OA-POSS) by means of electrostatic self-assembly for the development of a novel room-temperature phosphorescence sensor for DNA sensing in biological fluids (see graphic).
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paper_title: A systematic study on the growth of gaas nanowires by metal-organic chemical vapor deposition.

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The epitaxial growth of GaAs nanowires (NWs) on GaAs(111)B substrates by metal−organic chemical vapor deposition has been systematically investigated as a function of relevant growth parameters, namely, temperature, arsine (AsH3) and trimethyl-gallium (TMGa) flow rates, growth time, and gold nanoparticle catalyst size. When growing in excess As conditions (V/III molar ratios greater than four), the NW growth rate is independent of AsH3 concentration, while it is linearly dependent on TMGa concentration, and it is thermally activated. The NW morphology is primarily affected by the growth temperature, with very uniform NWs growing at around 400 °C and severely tapered NWs growing above 500 °C. A simple phenomenological expression that allows prediction of the NW growth rate over a wide range of growth parameters has been derived. The growth rate dependence on the seed nanoparticle size has also been investigated, which reveals valuable information on the role of catalyst supersaturation and Ga surface diffu...
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paper_title: DNA-repair and carcinogen-metabolising enzymes genetic polymorphisms as an independent risk factor for hepatocellular carcinoma in Caucasian liver-transplanted patients.

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We studied polymorphisms of three genes, UDP-glucuronosyltransferase1A7 (UGT1A7), Glutathione-S-transferaseM1 (GSTM1) and X-Ray Cross Complementing group 1 (XRCC1), involved in detoxification of xenobiotics or DNA-repair in a population of 133 liver-transplanted patients, including 56 patients with hepatocellular carcinoma (HCC) and 77 without HCC, and in 89 healthy controls originating from the south of France. Multiple logistic regression analysis showed that, among liver-transplanted patients, interactions between XRCC1-G/G or -G/A and GSTM1-nul polymorphisms were independently associated with hepatocellular carcinoma (p interaction=0.027) concurrently with increasing age (p<0.001), male sex (p=0.037) and chronic hepatitis B or C virus infection (p=0.018 and p=0.001 respectively). On the contrary, no relationship was observed between UGT1A7 polymorphisms considered alone or in interaction with GSTM1 or XRCC1 polymorphisms and HCC. This suggests that concomitant impaired metabolism of carcinogenic compounds and impaired DNA-repair function play an important role in liver carcinogenesis in high-risk cirrhotic patients originating from the south of France.
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paper_title: Readily reusable electrochemical DNA hybridization biosensor based on the interaction of DNA with single-walled carbon nanotubes.

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Carboxylic group-functionalized single-walled carbon nanotubes (SWNTs) were assembled vertically on the glassy carbon electrode using ethylenediamine as linking agent to fabricate an aligned electrode (SWNTE). Single-stranded DNA (ssDNA) wrapped around the SWNTs to form ssDNA-wrapped SWNTE structures based on the interaction between ssDNA and SWNT. A sensitive differential pulse voltammetric (DPV) response was obtained at the ssDNA-wrapped SWNTE owing to the electrooxidation of guanine bases. Double-stranded DNA (dsDNA) was formed when ssDNA on the ssDNA-wrapped SWNTE was hybridized with complementary ssDNA (cDNA). The dsDNA was removed from the SWNTs by undergoing a process of preconditioning at -0.6 V. Consequentially, the DPV response of guanine bases decreased. The used SWNTE could be renewed easily via ultrasonically rinsing. On the basis of this mechanism, a label-free and readily reusable electrochemical DNA hybridization biosensor was designed by directly monitoring the current change of guanine bases. Under optimum conditions, the plot of the measurement signal of guanine bases versus the cDNA concentrations was a good straight line in the range of 40-110 nM with a detection limit of 20 nM (3s). The biosensor can be switched to detect different target DNAs easily.
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paper_title: Self‐Assembled Multilayers of Polyethylenimine and DNA: Spectrophotometric and Electrochemical Characterization and Application for the Determination of Acridine Orange Interaction

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This work deals with the study of the interaction between acridine orange (AO) and calf-thymus double stranded DNA (dsDNA) present in supramolecular architectures built on gold electrodes modified with mercapto-1-propanesulfonic acid (MPS) by self-assembling of polyethylenimine and dsDNA. The optimal conditions for building the supramolecular architecture were obtained from UV-vis spectrophotometric experiments. The electrochemical studies were performed by adsorptive transfer square wave voltammetry from the evaluation of the oxidation signal of AO accumulated within the multistructure. The effect of the number of PEI-dsDNA bilayers (Au/MPS/(PEI-dsDNA)n) on the accumulation and electrooxidation of AO is also discussed.
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paper_title: A study of the interaction of rhodamine 6G with DNA by spectrophotometry and probe microscopy

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The interaction of rhodamine 6G with DNA was studied by the methods of spectrophotometry and scanning probe microscopy. It was ascertained that rhodamine 6G interacts with the DNA macromolecules by cooperative binding to the exterior surface of the polymeric chain. As a result, organic nanostructures form on the surface of the polymers. The number of dye molecules in the nanostructures is estimated. The distribution of these structures along the double helix of DNA and their merging into larger conglomerates is studied.
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paper_title: Electrochemical Detection and Control of Interactions between DNA and Electroactive Intercalator Using a DNA−Alginate Complex Film Modified Electrode

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The surface of a glassy carbon electrode was modified with a DNA-alginate complex film in which water-soluble DNA was encapsulated into a calcium-alginate gel. The resulting modified electrode (DAFE) was used to detect ethidium bromide (EtBr), after its accumulation on the electrode. The intercalative behavior of EtBr for dsDNA in the film was investigated by measuring the electrode response based on the intercalation of EtBr separated from nonspecific interactions (electrostatic interaction). The accumulation of EtBr in the dsDAF was enhanced by applying a negative potential below -200 mV at the dsDAFE. When a positive potential above +700 mV was applied to the dsDAFE for a constant time with stirring in a Tris buffer solution, the amount accumulated decreased. These results indicate that it is possible to electrochemically control the accumulation and release of EtBr when a dsDAFE is used. In addition, the accumulation and detection of EtBr in spiked river water samples and daunomycin, an antitumor agent, is described.
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paper_title: Development of DNA electrochemical biosensor based on covalent immobilization of probe DNA by direct coupling of sol-gel and self-assembly technologies.

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A new procedure for fabricating deoxyribonucleic acid (DNA) electrochemical biosensor was developed based on covalent immobilization of target single-stranded DNA (ssDNA) on Au electrode that had been functionalized by direct coupling of sol-gel and self-assembled technologies. Two siloxanes, 3-mercaptopropyltrimethoxysiloxane (MPTMS) and 3-glycidoxypropyltrimethoxysiloxane (GPTMS) were used as precursors to prepare functionally self-assembly sol-gel film on Au electrode. The thiol group of MPTMS allowed assembly of MPTMS sol-gel on gold electrode surface. Through co-condensation between silanols, GPTMS sol-gel with epoxide groups interconnected into MPTMS sol-gel and enabled covalent immobilization of target NH(2)-ssDNA through epoxide/amine coupling reaction. The concentration of MPTMS and GPTMS influenced the performance of the resulting biosensor due to competitive sol-gel process. The linear range of the developed biosensor for determination of complementary ssDNA was from 2.51 x 10(-9) to 5.02 x 10(-7)M with a detection limit of 8.57 x 10(-10)M. The fabricated biosensor possessed good selectivity and could be regenerated. The covalent immobilization of target ssDNA on self-assembled sol-gel matrix could serve as a versatile platform for DNA immobilization and fabrication of biosensors.
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paper_title: Electrochemical DNA biosensor for the study of ciprofloxacin-DNA interaction.

paper_content:

Abstract The interaction of ciprofloxacin with DNA was studied by using an electrochemical DNA biosensor. The binding mechanism of ciprofloxacin was elucidated by using constant current potentiometry and differential pulse voltammetry at DNA-modified glassy carbon electrode. The decrease in the guanine oxidation peak area or peak current at +0.9 V was used as an indicator for the interaction mechanism in 0.2 M acetate buffer (pH 5). The binding constant ( K ) values obtained were 1.33 ± 0.02 × 10 4 and 1.32 ± 0.08 × 10 4 M −1 with constant current potentiometry and differential pulse voltammetry, respectively. A linear dependence of the guanine peak area or peak currents was observed in the range of 40–80 μM ciprofloxacin, with a detection limit of 24 μM with r = 0.995 and 9 μM with r = 0.999 by using constant current potentiometry and differential pulse voltammetry, respectively. Moreover, the influence of sodium and calcium ions was also studied to elucidate the mechanism of ciprofloxacin–DNA interaction at different solution conditions, and this proved to be helpful in understanding the ciprofloxacin–DNA interaction.
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paper_title: Detection of DNA hybridization based on SnO2 nanomaterial enhanced fluorescence

paper_content:

In this paper, enhanced fluorescence emissions were firstly investigated based on SnO2 nanomaterial, and its application in the detection of DNA hybridization was also demonstrated. The microarray of SnO2 nanomaterial was fabricated by the vapour phase transport method catalyzed by patterned Au nanoparticles on a silicon substrate. A probe DNA was immobilized on the substrate with patterned SnO2 nanomaterial, respectively, by covalent and non-covalent linking schemes. When a fluorophore labelled target DNA was hybridized with a probe DNA on the substrate, fluorescence emissions were only observed on the surface of SnO2 nanomaterial, which indicated the property of enhancing fluorescence signals from the SnO2 nanomaterial. By comparing the different fluorescence images from covalent and non-covalent linking schemes, the covalent method was confirmed to be more effective for immobilizing a probe DNA. With the combined use of SnO2 nanomaterial and the covalent linking scheme, the target DNA could be detected at a very low concentration of 10 fM. And the stability of SnO2 nanomaterial under the experimental conditions was also compared with silicon nanowires. The findings strongly suggested that SnO2 nanomaterial could be extensively applied in detections of biological samples with enhancing fluorescence property and high stability.
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paper_title: Fabrication of micropatterned ZnO/SiO2 core/shell nanorod arrays on a nanocrystalline diamond film and their application to DNA hybridization detection

paper_content:

Micropatterned ZnO/SiO2 core/shell nanorod arrays are successfully fabricated on nanocrystalline diamond (NCD) film surfaces, and their performance as a fluorescence signal enhancing platform for DNA hybridization detection is also investigated. The fabrication process, from oriented ZnO nanorod deposition, amine silanation, and attachment of a biofunctional cross-linking molecule to the covalent immobilization of probe oligonucleotides, is defined. X-Ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) are used to characterize ZnO/SiO2 core/shell nanorods. The sequence complementary and stability of the DNA-modified surface are demonstrated in hybridization experiments. The use of ZnO/SiO2 nanorod arrays not only greatly enhances the fluorescence signal collected but also decreases the nonspecific adsorption effect of ZnO nanomaterials after carrying out the hybridization reaction.
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paper_title: Probing DNA Hybridization by Impedance Measurement Based on CdS-Oligonucleotide Nanoconjugates

paper_content:

A novel, sensitive DNA hybridization detection protocol, based on DNA-quantum dots nanoconjugates coupled with electrochemical impedance spectroscopy (EIS) detection, is described. The amino-linked ss-DNA probe was covalently immobilized onto a self-assembled mercaptoacetic acid monolayer modified gold electrode; after hybridization with the target ssDNA-CdS nanoconjugates, EIS was used to detect the change of interfacial electron-transfer resistance (Ret) of the redox marker, [Fe(CN)6]4−/3−, from solution to transducer surface. The results showed that when target ssDNA-CdS nanoconjugates hybridized with probe oligonucleotide, a double helix film formed on the electrode, a remarkably increased Ret value was observed. Only complementary DNA sequence had an obvious signal compared with three-base mismatched or non-completely matched sequences under the optimized experimental conditions. Due to having more negative charges, space resistance and the semiconductor property, CdS nanoparticle labels on target DNA could improve the sensitivity to two orders of magnitude when compared with non-CdS tagged DNA sequences.
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paper_title: Amplified electrochemical DNA-sensing of nanostructured metal oxide films deposited on disposable graphite electrodes functionalized by chemical vapor deposition

paper_content:

Abstract Metal oxide nanostructures offer interesting possibilities to design functional surfaces for bio-sensing applications, for instance, through higher surface area leading to enhanced immobilization of biomolecules, which increases the detection limit. Herein, an amplified electrochemical sensing method has been presented for the detection of DNA based on the readout resulting from chemical oxidation of guanine on nanoscaled metal oxides (TiO 2 , SnO 2 and Fe 3 O 4 ) obtained by chemical vapor deposition (CVD) onto pencil graphite electrode (PGE) as electrochemical transducer. The proposed strategy is suitable to produce cost-effective disposable sensor elements enabling quantitative detection of nanomolar concentrations of DNA. When preparing these metal oxide surfaces by CVD onto PGEs, the various experimental conditions; such as, the effect of different concentrations of 20 mer-bases DNA oligonucleotide (ODN20), and the surface pretreatment steps were studied to obtain better surface properties for DNA immobilization. The detection limit estimated for signal-to-noise ratios >3 corresponds to 21.3, 53.9 and 45.8 nmole/ml ODN20 concentrations for PGEs modified with TiO 2 , SnO 2 and Fe 3 O 4 films, respectively. The electrochemical detection of DNA onto metal oxide@PGEs is discussed together with the application potential.
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paper_title: Cadmium sulfide-modified GCE for direct signal-amplified sensing of DNA hybridization.

paper_content:

A novel DNA hybridization sensor based on nanoparticle CdS modified glass carbon electrode (GCE) was constructed and characterized coupled with Cyclic Voltammogram (CV) and Differential Pulse Voltammogram (DPV) techniques. The mercapto group-linked probe DNA was covalently immobilized onto the CdS layer and exposed to oligonucleotide (ODN) target for hybridization. The structure of DNA sensor was characterized by X-ray diffraction (XRD), field-emission microscopy (FESEM) and X-ray photoelectron spectra (XPS). Sensitive electrical readout achieved by CV and DPV techniques shown that when the target DNA hybridized with probe CdS-ODN conjugates and the double helix formed on the modified electrode, a significant increased response was observed comparing with the bare electrodes. The selectivity of the sensor was tested using a series of matched and certain-point mismatched sequences with concentration grads ranging from 10(-6) microM to 10(1) microM. The signal was in good linear with the minus logarithm of target oligonucleotide concentration with detection limit <1 pM and the optimized target DNA concentration was 10(-6) microM for the signal amplification. Due to great surface properties, the additional negative charges and space resistance of as-prepared CdS nanoparticles, the sensor was able to robustly discriminate the DNA hybridization responses with good sensitivity and stability.
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paper_title: Enhanced mass sensitivity of ZnO nanorod-grown quartz crystal microbalances

paper_content:

Abstract ZnO nanorods were directly grown on the surface of a quartz crystal in zinc nitrate hexahydrate solution. The nanorod dimensions were controlled by varying the growth time, from 0.6 μm for a growth time of 1 h to 2.0 μm after 3 h of growth. After sequentially coating the nanorod-grown quartz crystals with thin layers of titanium and gold by thermal evaporation, the crystals were exposed to mercaptohexanol solution and the frequency change due to mercaptohexanol adsorption was determined. The frequency change for the nanorod-grown quartz crystal was about 60 times greater than that of the corresponding plain gold-coated quartz crystal due to the increase in surface area afforded by the nanorods. A similar enhancement of mass sensitivity was observed for the immobilization and hybridization of oligonucleotides on the nanorod-grown crystals. Although for larger molecules the enhancement of mass sensitivity was degraded by steric hindrance, the results demonstrate the potential of ZnO nanorod-grown quartz crystals for use in DNA-based biosensor applications.
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paper_title: Cell-penetrating quantum dots based on multivalent and endosome-disrupting surface coatings.

paper_content:

We report the development of cell-penetrating quantum dots (QDs) based on the use of multivalent and endosome-disrupting (endosomolytic) surface coatings. Hyperbranched copolymer ligands such as polyethylene glycol (PEG) grafted polyethylenimine (PEI-g-PEG) are found to encapsulate and solubilize luminescent quantum dots through direct ligand-exchange reactions. Because of the positive charges and a “proton sponge effect” associated with multivalent amine groups, this class of ligand-exchanged QDs is able to penetrate cell membranes and is also able to disrupt endosomal organelles in living cells. The grafted PEG segment is essential for reducing the cytotoxicity of PEI as well as for improving the overall nanoparticle stability and biocompatibility. In comparison with previous QDs encapsulated with amphiphilic polymers, the cell-penetrating QDs are smaller in size and are considerably more stable in acidic environments. Cellular uptake and imaging studies reveal that the number of PEG grafts per PEI mole...
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paper_title: Multiplexed Hybridization Detection with Multicolor Colocalization of Quantum Dot Nanoprobes

paper_content:

We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized quantum dots as nanoprobes. In the presence of various target sequences, combinatorial self-assembly of the nanoprobes via independent hybridization reactions leads to the generation of discernible sequence-specific spectral codings. Detection of single-molecule hybridization is achieved by measuring colocalization of individual nanoprobes. Genetic analysis for anthrax pathogenicity through simultaneous detection of multiple relevant sequences is demonstrated using this novel biosensing method as proof-of-concept.
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paper_title: A novel FRET-based optical fiber biosensor for rapid detection of Salmonella typhimurium.

paper_content:

A biosensor that is portable and permits on-site analysis of samples would significantly reduce the large economical burden of food products recalls. A fiber optic portable biosensor utilizing the principle of fluorescence resonance energy transfer (FRET) was developed for fast detection of Salmonella typhimurium (S. typhimurium) in ground pork samples. Labeled antibody-protein G complexes were formed via the incubation of anti-Salmonella antibodies labeled with FRET donor fluorophores (Alexa Fluor 546) and protein G (PG) labeled with FRET acceptor fluorophores (Alexa Fluor 594). Utilizing silanization, the labeled antibodies-PG complexes were then immobilized on decladded, tapered silica fiber cores to form the evanescent wave-sensing region. The biosensors were tested in two different solutions: (1) PBS doped with S. typhimurium and (2) homogenized pork sample with S. typhimurium. The fiber probes tested in a S. typhimurium doped phosphate buffered solution demonstrated the feasibility of the biosensor for detecting S. typhimurium as well as determined the optimal packing density of the labeled antibody-PG complexes on the surface of fibers. The results showed that a packing density of 0.033 mg/ml produced the lowest limit of detection of 10(3)cells/ml with 8.2% change in fluorescence. The fiber probes placed in homogenized pork samples inoculated with S. typhimurium showed a limit of detection of 10(5)CFU/g with a 6.67% in fluorescence within a 5-min response time. These results showed that the FRET-based fiber optic biosensor can become a useful analytical tool for detection of S. typhimurium in real food samples.
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paper_title: Nonradiative resonant excitation transfer from nanocrystal quantum dots to adjacent quantum channels.

paper_content:

Evidence is provided for nonradiative resonant energy transfer (NRET) from excitons in nanocrystal quantum dots (NCQDs) to the confined states of an adjacent quantum well (QW) at low excitation power and rate competitive with the quantum dot radiative decay. This indicates that NRET in optimized NCQD−QW/nanowire systems may provide a solar energy conversion approach with a viable tradeoff with the bottlenecks of charge carrier generation and/or transport to/in electrodes faced by excitonic solar cells.
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paper_title: A Progress in Detection of Interactions Between Macromolecules: Linked FRET Using Three Color Fluorophore

paper_content:

Fluorescence resonance energy transfer (FRET) is the energy transfer from an activated donor fluorophore to a receiving fluorophore. The efficiency of the energy transfer is the function of the distance between the two fluorophores, and is very sensitive to the distance. Its effective response distance is between 1~10 nm, thus it can be used to measure the distance between atoms or molecules. The feature of FRET is very useful in researches on conformational changes, interaction between macromolecules and signal transductions within live cells, and FRET has become a powerful tool in biomedical investigations. However, biological processes often involve interactions between more than two macromolecules, and FRET using two color fluorophores cannot meet the research demand. Recently, two research groups made breakthrough, establishing a novel FRET technique using three color fluorophores based on confocol microscopy and flow cytometry, respectively. The invention will significantly advance researches in biological and related fields.
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paper_title: Multiplexed Hybridization Detection of Quantum Dot-Conjugated DNA Sequences Using Surface Plasmon Enhanced Fluorescence Microscopy and Spectrometry

paper_content:

In this study, the general suitability of quantum dot (QD)−DNA conjugates for the surface plasmon enhanced fluorescence spectroscopy technique is demonstrated. Furthermore, the QD−DNA system is transferred to the platform of surface plasmon enhanced fluorescence microscopy. Using this technique together with a microarray format, in which the sensor-bound single-stranded catcher probes are organized in individual surface spots, results in a simultaneous qualitative analysis of QD-conjugated analyte DNA strands as multicolor images. A clear decomposition of different QDx−DNAy mixtures can be achieved for sequential, as well as mixture injections. Besides this, the study describes the successful approach of measuring spectrally resolved surface plasmon enhanced fluorescence signals derived from catcher probe hybridized QD−DNA conjugates.
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paper_title: Graded-Bandgap Quantum- Dot-Modified Nanotubes: A Sensitive Biosensor for Enhanced Detection of DNA Hybridization†

paper_content:

Biosensors containing quantum dots (QDs) as fluorescent markers have been employed for immunoassays, gene expression, genomic analysis, and fluorescence imaging because QDs have superior properties to traditional organic fluorophores, such as higher quantum yield and much sharper emission spectra. Recently, the use of QDs as fluorescence resonance energy transfer (FRET) donors to detect DNA, RNA, or proteins was reported, where an amplification of the detected fluorescent signal was achieved by exploiting FRET. One particularly promising strategy in this context involves funneling energy from strongly light-harvesting species towards a reaction center, because energy is always transferred from a species with a larger bandgap to a species with a smaller bandgap. In this way, a cascaded-energy-transfer structure based on QD assembly has been constructed with a high photoluminescence (PL) intensity originating from the center layer. The use of QDs as biomarkers to functionalize nanotubes (NTs) has been also reported, as a new and active field of research. It is known that the preparation of functionalized NTs, for example, inside an ordered porous alumina membrane, can yield hybrid systems containing a large number of aligned and functionalized channels for biological applications. For example, NTs functionalized with QDs have found promising applications as drug carriers, biomarkers, and biosensors. Hence, taking advantage of the superior properties of QDs described above, we describe in this Communication a novel approach to designing functionalized NTs with a cascaded-energy-transfer architecture by incorporating graded-bandgap QDs into ordered porous alumina membranes (Scheme 1) and their use as highly sensitive biosensor component for the detection of DNA hybridization through energy transfer. The incorporation of QDs into the NTs was performed by the well-known approach of layer-by-layer (LBL) deposition. Mercaptoundecanoic acid (MPA) ligand coated ZnCdSe alloy QDs with luminescence maxima at k= 561 nm (QD) (d = 6.6 nm), 594 nm (QD) (d = 6.1 nm), and 614 nm (QD) (d = 5.5 nm) were used. Their PL emission and UV absorption spectra of aqueous suspensions are shown in Figure 1A and Figure S1 (Supporting Information), respectively. Several advantages of ZnCdSe alloy QDs compared with other types of QDs, for example, core/shell QDs, are summarized here: 1) There are very few surface defects around the luminescent particles owing to the high crystallinity. 2) They have large particle sizes, hardened lattice structures, and decreased interdiffusion. 3) ZnCdSe alloy QDs can produce atomically abrupt jumps in the chemical potential, which can further localize free exciton states in the alloy crystallites. Therefore, the fluorescence stability of ZnCdSe alloy QDs can be greatly improved. As a matrix forming the walls of the NTs we used globular N,N-disubstituted hydrazine phosphorus-containing dendrimers of the fourth generation having 96 terminal groups with either cationic [G4(NH Et2Cl )96] (G4 ) or anionic [G4(CHCOONa)96] (G4 ) character. The two dendrimers possess a controlled shape and well-defined external and internal surfaces. The multilayer structures consisting of the two dendritic polyelectrolytes show a lower degree of interpenetration than multilayer systems composed of common linear polyelectrolytes. Therefore, they are ideal components for constructing compartmentalized NT walls, in which different functional species, such as water-soluble QDs with different size or composition in the case of the alloy particles used in this experiment, can be deposited with high spatial precision. For LBL deposition in an ordered porous alumina membrane, the pore walls were first coated with the positively charged 3-aminopropyl dimethylethoxysilane (3-APS), further allowing the deposition of a negatively charged denC O M M U N IC A IO N
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paper_title: Single-Molecule Quantum-Dot Fluorescence Resonance Energy Transfer

paper_content:

Colloidal semiconductor quantum dots are promising for single-molecule biological imaging due to their outstanding brightness and photostability. As a proof of concept for single-molecule fluorescence resonance energy transfer (FRET) applications, we measured FRET between a single quantum dot and a single organic fluorophore Cy5. DNA Holliday junction dynamics measured with the quantum dot/Cy5 pair are identical to those obtained with the conventional Cy3/Cy5 pair, that is, conformational changes of individual molecules can be observed by using the quantum dot as the donor.
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paper_title: Quenching of CdSe quantum dot emission, a new approach for biosensing.

paper_content:

The emission of CdSe quantum dots linked to the 5'-end of a DNA sequence is efficiently quenched by hybridisation with a complementary DNA strand with a gold nanoparticle attached at the 3'-end; contact of the quantum dot and gold nanoparticle occurs.
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paper_title: Magnetic field control of exchange and noise immunity in double quantum dots.

paper_content:

We employ density functional calculated eigenstates as a basis for exact diagonalization studies of semiconductor double quantum dots, with two electrons, through the transition from the symmetric bias regime to the regime where both electrons occupy the same dot. We calculate the singlet−triplet splitting J(e) as a function of bias detuning e and explain its functional shape with a simple, double anticrossing model. A voltage noise suppression “sweet spot,” where dJ(e)/de = 0 with nonzero J(e), is predicted and shown to be tunable with a magnetic field B.
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paper_title: DNA Hybridization Detection with Blue Luminescent Quantum Dots and Dye-Labeled Single-Stranded DNA

paper_content:

A simple DNA sensing platform was developed based on the fluorescence resonance energy transfer (FRET) between blue-luminescent CdTe QDs and dye-labeled ssDNA. A cationic polymer acts as a “bridge” to bring the donor to acceptor together and achieves the high FRET efficiency. The hybridization event was recognized by the different FRET efficiencies due to different interaction abilities of single-stranded and double-stranded DNA with the polymer. This platform provides a homogeneous DNA assay that takes advantage of the fluorescence detection method, but with minimal DNA modification.
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paper_title: Compact quantum dot probes for rapid and sensitive DNA detection using highly efficient fluorescence resonant energy transfer

paper_content:

We developed a simple method for quickly synthesizing compact quantum dot (QD)–DNA probes for sensitive DNA detection using fluorescence resonant energy transfer (FRET). The density of DNA probes on the QD surface was controlled to avoid steric hindrance and to promote rapid hybridization with target DNA molecules. The radius of the final QDs was only around 3 nm after applying the functional coating, enabling highly efficient energy transfer. It was demonstrated that nearly 70% transfer efficiency could be achieved with only a few DNA molecules on each QD and that the FRET-based DNA detection could be carried out within 10 min with a sub-nM detection limit. Theoretical analysis was also performed to confirm our results.
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paper_title: Semiconductor quantum dots as two-photon sensitizers.

paper_content:

This study presents the potential of quantum dots as two-photon sensitizers for attached energy acceptors. With two-photon absorption cross sections, which are orders of magnitudes higher than those of any molecule, quantum dots constitute outstanding NIR sensitizers. The successful energy transfer to conjugated phthalocyanines was demonstrated using two-photon excitation of the quantum dots with a 1100 nm wavelength and was monitored with femtosecond time-resolved pump−probe spectroscopy.
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paper_title: Fluorescence in situ hybridization (FISH) on maize metaphase chromosomes with quantum dot-labeled DNA conjugates

paper_content:

Semiconductor nanocrystals, also called quantum dots (QDs), are novel inorganic fluorophores which are brighter and more photostable than organic fluorophores. In the present study, highly dispersive QD-labeled oligonucleotide (TAG)(8) (QD-deoxyribonucleic acid [DNA]) conjugates were constructed via the metal-thiol bond, which can be used as fluorescence in situ hybridization (FISH) probes. FISH analysis of maize metaphase chromosomes using the QD-DNA probes showed that the probes could penetrate maize chromosomes and nuclei and solely hybridized to complementary target DNAs. Compared with the conventional organic dyes such as Cy3 and fluorescein isothiocyanate, this class of luminescent labels bound with oligonucleotides is brighter and more stable against photobleaching on the chromosomes after FISH. These results suggest that QD fluorophores may be a more stable and useful fluorescent label for FISH applications in plant chromosome mapping considering their size-tunable luminescence spectra.
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paper_title: Synthesis of cadmium telluride quantum wires and the similarity of their effective band gaps to those of equidiameter cadmium telluride quantum dots.

paper_content:

High-quality colloidal CdTe quantum wires having purposefully controlled diameters in the range 5-11 nm are grown by the solution-liquid-solid (SLS) method, using Bi nanoparticle catalysts, cadmium octadecylphosphonate and trioctylphosphine telluride as precursors, and a TOPO solvent. The wires adopt the wurtzite structure and grow along the [002] direction (parallel to the c axis). The size dependence of the effective band gaps in the wires is determined from the absorption spectra and compared to the experimental results for high-quality CdTe quantum dots. In contrast to the predictions of an effective-mass approximation, particle-in-a-box model, and previous experimental results from CdSe and InP dot-wire comparisons, the effective band gaps of CdTe dots and wires of like diameter are found to be experimentally indistinguishable. The present results are analyzed using density functional theory under the local-density approximation by implementing a charge-patching method. The higher-level theoretical analysis finds the general existence of a threshold diameter, above which dot and wire effective band gaps converge. The origin and magnitude of this threshold diameter are discussed.
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paper_title: Quantum dots: Resonant energy-transfer sensor

paper_content:

The potential uses of inorganic quantum dots in biolabelling and sensing could be expanded through their ability to function as resonant energy-transfer donors. Novel quantum dot–protein sensors may be the way ahead.
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paper_title: Multicolour hybrid nanoprobes of molecular beacon conjugated quantum dots: FRET and gel electrophoresis assisted target DNA detection

paper_content:

We have developed multicolour hybrid DNA probes employing green, yellow and orange colour quantum dot conjugated molecular beacons with black hole quencher 2. Optical and electrophoretic characterization revealed fluorescent energy transfer that follows the FRET mechanism with single nucleotide discrimination. Target DNA identification was observed to be highly sensitive up to 8 ng in gel electrophoresis. Comparison with the conventional organic dye SYBR Gold™ showed that our hybrid nanoprobes exhibit more stable performance with less background signal.
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paper_title: Studies of a viral suppressor of RNA silencing p19-CFP fusion protein: A FRET-based probe for sensing double-stranded fluorophore tagged small RNAs

paper_content:

Eukaryotes have evolved complex cellular responses to double-stranded RNA. One response that is highly conserved across many species is the RNA silencing pathway. Tombusviruses have evolved a mechanism to evade the RNA silencing pathway that involves a small protein, p19, that acts as a suppressor of RNA silencing. This protein binds specifically to small-interfering RNAs (siRNAs) with nanomolar affinity in a sequence-independent manner and with size selectivity.
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paper_title: Quantitative FRET Analysis by Fast Acquisition Time Domain FLIM at High Spatial Resolution in Living Cells

paper_content:

Quantitative analysis in Forster resonance energy transfer (FRET) experiments in live cells for protein interaction studies is still a challenging issue. In a two-component system (FRET and no FRET donor species), fitting of fluorescence lifetime imaging microscopy (FLIM) data gives the fraction of donor molecules involved in FRET (fD) and the intrinsic transfer efficiency. But when fast FLIM acquisitions are used to monitor dynamic changes in protein-protein interactions at high spatial and temporal resolutions in living cells, photon statistics and time resolution are limited. In this case, fitting procedures are not reliable, even for single lifetime donors. We introduce the new concept of a minimal fraction of donor molecules involved in FRET (mfD), coming from the mathematical minimization of fD. We find particular advantage in the use of mfD because it can be obtained without fitting procedures and it is derived directly from FLIM data. mfD constitutes an interesting quantitative parameter for live cell studies because it is related to the minimal relative concentration of interacting proteins. For multi-lifetime donors, the process of fitting complex fluorescence decays to find at least four reliable lifetimes is a near impossible task. Here, mfD extension for multi-lifetime donors is the only quantitative determinant. We applied this methodology for imaging the interaction between the bromodomains of TAFII250 and acetylated histones H4 in living cells at high resolution. We show the existence of discrete acetylated chromatin domains where the minimal fraction of bromodomain interacting with acetylated H4 oscillates from 0.26 to 0.36 and whose size is smaller than half of one micron cube. We demonstrate that mfD by itself is a useful tool to investigate quantitatively protein interactions in live cells, especially when using fast FRET-FLIM acquisition times.
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paper_title: In vitro derby imaging of cancer biomarkers using quantum dots.

paper_content:

Semiconductor quantum dots (QDs), which have broad absorption with narrow emission spectra, are useful for multiplex imaging. Here, fluorescence derby imaging using dual color QDs conjugated by the AS1411 aptamer (targeting nucleolin) and the arginine–glycine–aspartic acid (targeting the integrin αvβ3) in cancer cells is reported. Simultaneous fluorescence imaging of cellular distribution of nucleolin and integrin αvβ3 using QDs enables easy monitoring of separate targets in the cancer cells and the normal healthy cells. These results suggest the feasibility of a concurrent visualization of QD-based multiple cancer biomarkers using small molecules such as aptamer or peptide ligands.
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paper_title: Effect of Surfactant on FRET and Quenching in DNA Sequence Detection Using Conjugated Polymers

paper_content:

The effect of a nonionic surfactant on various energy-transfer and quenching processes in deoxyribonucleic acid (DNA) sequence detection using the cationic conjugated polymer (CCP) poly{[9,9-bis(N,N,N-trimethylammonium)hexylfluorene]-co-1,4-phenylene diiodide) and peptide nucleic acid labeled with fluorescein (PNA-Flu*) has been investigated. Steady-state and time-resolved measurements reveal that nonionic surfactant enhances both sensitivity and selectivity in targeted DNA sequence detection. The enhancement of the sensitivity is ascribed to an increase in the CCP quantum yield due to the surfactant breaking up polymer aggregates, increasing the isolated polymer chain concentration, and reducing interchain quenching. This also increases the polymer surface-to-volume ratio. The sensitivity is also improved as the surfactant reduces CCP quenching by DNA and buffer solution through incorporation of the CCP in micelles, which reduces charge-transfer processes. Enhancement of the selectivity is achieved through the reduction of the hydrophobic interaction between the CCP and free PNA-Flu*. Time-resolved fluorescence lifetime analysis provides an effective way to differentiate these particular effects in the DNA-PNA-Flu assays. Comparing the decay profiles of the CCP, CCP/DNA, and CCP/complementary DNA:PNA-Flu*, it was found that both surfactant and DNA do not alter dramatically the isolated polymer chain lifetime (the first increases the concentration of the single chains by breaking up the polymer aggregation and the latter reduces the concentration of the isolated polymer chain by static quenching), therefore the change in the isolated polymer chain fluorescence lifetime can predominantly reflect the quenching of the donor by FRET to the PNA fluorescent label. Here, surfactant increases Forster radius by enhancing the polymer fluorescence quantum yield. Furthermore, surfactant also increases the difference in the donor lifetimes between the complementary and noncomplementary cases. This difference reflects the increase in the energy-transfer efficiency and hence higher selectivity. Fluorescein quenching is mediated by the CCP which causes Flu*-Flu* self-quenching via a PNA-CCP hydrophobic interaction. Optimization or minimization of various interactions to achieve the best DNA detection sensor is discussed.
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paper_title: Probing protein folding using site-specifically encoded unnatural amino acids as FRET donors with tryptophan.

paper_content:

The experimental study of protein folding is enhanced by the use of nonintrusive probes that are sensitive to local conformational changes in the protein structure. Here, we report the selection of an aminoacyl-tRNA synthetase/tRNA pair for the cotranslational, site-specific incorporation of two unnatural amino acids that can function as fluorescence resonance energy transfer (FRET) donors with Trp to probe the disruption of the hydrophobic core upon protein unfolding. l-4-Cyanophenylalanine (pCNPhe) and 4-ethynylphenylalanine (pENPhe) were incorporated into the hydrophobic core of the 171-residue protein, T4 lysozyme. The FRET donor ability of pCNPhe and pENPhe is evident by the overlap of the emission spectra of pCNPhe and pENPhe with the absorbance spectrum of Trp. The incorporation of both unnatural amino acids in place of a phenylalanine in the hydrophobic core of T4 lysozyme was well tolerated by the protein, due in part to the small size of the cyano and ethynyl groups. The hydrophobic nature of the ethynyl group of pENPhe suggests that this unnatural amino acid is a more conservative substitution into the hydrophobic core of the protein compared to pCNPhe. The urea-induced disruption of the hydrophobic core of the protein was probed by the change in FRET efficiency between either pCNPhe or pENPhe and the Trp residues in T4 lysozyme. The methodology for the study of protein conformational changes using FRET presented here is of general applicability to the study of protein structural changes, since the incorporation of the unnatural amino acids is not inherently limited by the size of the protein.
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paper_title: Single-quantum-dot-based DNA nanosensor

paper_content:

Rapid and highly sensitive detection of DNA is critical in diagnosing genetic diseases. Conventional approaches often rely on cumbersome, semi-quantitative amplification of target DNA to improve detection sensitivity. In addition, most DNA detection systems (microarrays, for example), regardless of their need for target amplification, require separation of unhybridized DNA strands from hybridized stands immobilized on a solid substrate, and are thereby complicated by solution–surface binding kinetics1,2. Here, we report an ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) capable of detecting low concentrations of DNA in a separation-free format. This system uses quantum dots (QDs)3,4,5 linked to DNA probes to capture DNA targets. The target strand binds to a dye-labelled reporter strand thus forming a FRET donor–acceptor ensemble. The QD also functions as a concentrator that amplifies the target signal by confining several targets in a nanoscale domain. Unbound nanosensors produce near-zero background fluorescence, but on binding to even a small amount of target DNA (∼50 copies or less) they generate a very distinct FRET signal. A nanosensor-based oligonucleotide ligation assay has been demonstrated to successfully detect a point mutation6 typical of some ovarian tumours in clinical samples.
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paper_title: Effects of Andreev reflection on the conductance of quantum-chaotic dots

paper_content:

We investigate the conductance statistics of a quantum-chaotic dot\char22{}a normal-metal grain\char22{}with a superconducting lead attached to it. The cases of one and two normal leads additionally attached to the dot are studied. For these two configurations the complete distribution of the conductance is calculated, within the framework of random matrix theory, as a function of the transparency parameter of the Schottky barrier formed at the interface of the normal-metal and superconducting regions. Our predictions are verified by numerical simulations.
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paper_title: High quality InAs quantum dots grown on patterned Si with a GaAs buffer layer

paper_content:

Ordered and dense InAs quantum dots grown on patterned Si(100) with a thin GaAs buffer layer have been investigated by transmission electron microscopy and electron energy loss spectroscopy. {111} faceted InAs quantum dots with good crystallinity were observed on top of the underlying GaAs buffer layer. It was revealed that the GaAs buffer layer and the lateral expansion of InAs have played key roles in releasing the misfit strain between InAs and Si and suppressing the formation of lattice defects in InAs quantum dots. These results suggest a possible pathway for the strain relaxation in the formation of quantum dots.
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paper_title: DNA biosensor based on chitosan film doped with carbon nanotubes.

paper_content:

A biosensor based on chitosan doped with carbon nanotube (CNT) was fabricated to detect salmon sperm DNA. Methylene blue (MB) was employed as a DNA indicator. It was found that CNTs can enhance the electroactive surface area threefold (0.28 +/- 0.03 and 0.093 +/- 0.06 cm(2) for chitosan-CNT- and chitosan-modified electrodes, respectively) and can accelerate the rate of electron transfer between the redox-active MB and the electrode. A low detection limit of 0.252 nM fish sperm DNA was achieved, and no interference was found in the presence of 5 microg/ml human serum albumin. The differential pulse voltammetry signal of MB was linear over the fish sperm DNA concentration range of 0.5-20 nM.
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paper_title: Enhanced resonance light scattering based on biocatalytic growth of gold nanoparticles for biosensors design

paper_content:

Abstract The biocatalytic growth of gold nanoparticles (Au-NPs) has been employed in the design of new optical biosensors based on the enhanced resonance light scattering (RLS) signals. Both absorption spectroscopy and transmission electron microscopy (TEM) analysis revealed Au-NP seeds could be effectively enlarged upon the reaction with H 2 O 2 , an important metabolite that could be generated by many biocatalytic reactions. Upon the stepwise enlargement of Au-NPs, the light scattering intensity could be greatly enhanced, which then allowed the quantitative detection of the analyte, H 2 O 2 . Further combination of the biocatalytic reaction that can yield H 2 O 2 by using the enzyme, glucose oxidase, with the enlargement of Au-NPs enabled the design of a sensitive glucose biosensor using the RLS technique. In the present study, we could achieve the detection of glucose in a linear range of 1.0 × 10 −6 M to 1.1 × 10 −4 M, with detection limit of 6.8 × 10 −7 M.
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paper_title: Hybridization sensing by electrical enhancement with nanoparticles in nanogap

paper_content:

In this work, the monolayer of gold nanoparticles within 72nm gap has been proposed to function as a DNA sensor. The authors suggest that the nanoparticles in the nanogap could act as hopping sites which amplify the conductance of hybridized DNA strands. The conductance amplification between single strand and hybridized DNAs through gold nanoparticles is observed. Various concentrations of capture and target DNA are discussed for optimal hybridization sensing purpose. With the help of 1nM capture DNAs, this sensor is able to analyze target DNA sequences at very low concentration of 1fM. Furthermore, by means of adjusting the denature temperature to 60°C, even single mismatch hybridization could be discriminated.In this work, the monolayer of gold nanoparticles within 72nm gap has been proposed to function as a DNA sensor. The authors suggest that the nanoparticles in the nanogap could act as hopping sites which amplify the conductance of hybridized DNA strands. The conductance amplification between single strand and hybridized DNAs through gold nanoparticles is observed. Various concentrations of capture and target DNA are discussed for optimal hybridization sensing purpose. With the help of 1nM capture DNAs, this sensor is able to analyze target DNA sequences at very low concentration of 1fM. Furthermore, by means of adjusting the denature temperature to 60°C, even single mismatch hybridization could be discriminated.
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paper_title: Surface-enhanced fluorescence of fluorescein-labeled oligonucleotides capped on silver nanoparticles.

paper_content:

Tiopronin monolayer-protected silver nanoparticles with different core sizes (average diameter = 2, 5, 20 nm) were prepared by using different mole ratios of silver nitrate/tiopronin. Ligands on the silver particles were partially displaced by fluorescein-labeled thiolate single-stranded oligonucleotides or their complementary unlabeled oligonucleotides through ligand exchange. The fluorophores on silver particles showed a surface-enhanced fluorescence (SEF) dependent on the size of metallic cores. The particles could be coupled through hybridizations of oligonucleotides bound on the particles. The coupled particles were aggregated due to multiple displacements of oligonucleotides on each particle, resulting in stronger SEF. The dye-labeled oligonucleotides were assembled on the silver islands on the solid substrate, and the complementary oligonucleotide-displaced particles were coupled via oligonucleotide hybridization. The couplings between particles and islands resulted in an obvious fluorescence enhancement.
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paper_title: Enhancement of DNA immobilization and hybridization on gold electrode modified by nanogold aggregates

paper_content:

Abstract Gold electrodes modified by nanogold aggregates (nanogold electrode) were obtained by the electrodeposition of gold nanoparticles onto planar gold electrode. The Electrochemical response of single-stranded DNA (ssDNA) probe immobilization and hybridization with target DNA was measured by cyclic voltammograms (CV) using methylene blue (MB) as an electroactive indicator. An improving method using long sequence target DNA, which greatly enhanced the response signal during hybridization, was studied. Nanogold electrodes could largely increase the immobilization amount of ssDNA probe. The hybridization amount of target DNA could be increased several times for the manifold nanogold electrodes. The detection limit of nanogold electrode for the complementary 16-mer oligonucleotide (target DNA1) and long sequence 55-mer oligonucleotide (target DNA2) could reach the concentration of 10 −9 mol/L and 10 −11 mol/L, respectively, which are far more sensitive than that of the planar electrode.
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paper_title: Enhancement of Electrocatalytic Activity of DNA-Conjugated Gold Nanoparticles and Its Application to DNA Detection

paper_content:

Hydrazine electrooxidation readily occurs on bare Au nanoparticles (AuNPs), whereas it does not on DNA-conjugated AuNPs. Thus, when DNA-conjugated AuNPs are used as electrocatalytic labels in electrochemical DNA detection, anodic current of hydrazine is not easily observed within the potential window because of the high overpotential caused by the slow electron-transfer kinetics on DNA-conjugated AuNPs as well as the slow electron tunneling between the AuNP and the indium−tin oxide (ITO) electrode. NaBH4 treatment significantly enhances the electrocatalytic activity of DNA-conjugated AuNPs. This enhancement substantially decreases the overpotential caused by the slow electron-transfer kinetics, and the anodic current of hydrazine can be measured within the potential window if the distance between the AuNP and the ITO electrode is not too large. The enhancement with NaBH4 treatment allows high signal current, and the low intrinsic electrocatalytic activity of ITO electrodes allows low background current. T...
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paper_title: Enhanced DNA detection based on the amplification of gold nanoparticles using quartz crystal microbalance

paper_content:

Gold nanoparticles were used as mass amplifiers to improve the frequency signal of QCM detection of DNA. Indirect labelling and direct labelling of DNA probes with gold nanoparticles was studied. Two-times amplification of gold nanoparticles was carried out to further improve the detection signal. It was suggested that the frequency shift of the indirect-labelling method was much more significant than that of the direct-labelling method. The detection limit of one-time amplification and two-times amplification detection of a 33-base oligonucleotide was 100 and 10 fM, respectively. Under corresponding sensitivity, the one-base mismatched DNA and complementary DNA could be distinguished clearly. As an example, the two-times amplification detection of 677TT gene type validated that the ratio of frequency shift for a complementary DNA: one-base-mismatched one was 2.1:1 under the detection limit of 10 fM.
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paper_title: Magnetic core-shell Fe3O4@Ag nanoparticles coated carbon paste interface for studies of carcinoembryonic antigen in clinical immunoassay.

paper_content:

This study demonstrates a novel approach toward development of advanced immunosensors based on chemically functionalized core-shell Fe3O4@Ag magnetic nanoparticles, and the preparation, characterization, and measurement of relevant properties of the immunosensor useful for the detection of carcinoembryonic antigen (CEA) in clinical immunoassay. The immunosensor based on the combination of a magnetic nanocore and an Ag metallic shell shows good adsorption properties for the attachment of the CEA antibody selective to CEA. The core-shell nanostructure presents good magnetic properties to facilitate and modulate the way it was integrated into a carbon paste. Under optimal conditions, the resulting composite presents good electrochemical response for the detection of CEA, and allows detection of CEA at a concentration as low as 0.5 ng.mL(-1). Importantly, the proposed methodology could be extended to the detection of other antigens or biocompounds.
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paper_title: Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles

paper_content:

The effects of metal-enhanced fluorescence (MEF) have been measured for two dyes commonly used in DNA microarrays, Cy3 and Cy5. Silver island films (SIFs) grown on glass microscope slides were used as substrates for MEF DNA arrays. We examined MEF by spotting biotinylated, singly-labeled 23 bp DNAs onto avidin-coated SIF substrates. The fluorescence enhancement was found to be dependent on the DNA spotting concentration: below ∼12.5 μM, MEF increased linearly, and at higher concentrations MEF remained at a constant maximum of 28-fold for Cy5 and 4-fold for Cy3, compared to avidin-coated glass substrates. Hybridization of singly-labeled oligonucleotides to arrayed single-stranded probes showed lower maximal MEF factors of 10-fold for Cy5 and 2.5-fold for Cy3, because of the smaller amount of immobilized fluorophores as a result of reduced surface hybridization efficiencies. We discuss how MEF can be used to increase the sensitivity of DNA arrays, especially for far red emitting fluorophores like Cy5, without significantly altering current microarray protocols.
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paper_title: Fabrication of the nanogapped gold nanoparticles film for direct electrical detection of DNA and EcoRI endonuclease.

paper_content:

In situ seeding growth of gold nanoparticles (AuNPs) by the reaction of HAuCl4 and NH2OH has been employed in the fabrication of the nanogapped AuNPs film for direct electrical detection of DNA hybridization and DNA cleavage by EcoRI endonuclease. The distance between neighboring gold nanoparticles is less than the length of the probe DNA, implying that the DNA strand could bridge the AuNPs to provide an electron tunneling path between microelectrodes. The double-stranded DNA (dsDNA) formed by hybridization of probe and target DNA is detected by current-voltage (I-V) curve measurements. When dsDNA is cleaved by restriction endonuclease EcoRI, the electron tunneling path can be cut off, which is reflected from the different slopes of I-V curves between dsDNA and dsDNA cleavage by EcoRI in the label-free electrical measurements. The novel and simple method of fabricating the nanogapped AuNPs film by in situ seeding growth could provide a promising bioanalytical platform for studying both DNA-DNA and DNA-protein interactions.
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paper_title: Enhanced photoelectrochemical method for linear DNA hybridization detection using Au-nanopaticle labeled DNA as probe onto titanium dioxide electrode.

paper_content:

A photoelectrochemical method was proposed to detect DNA hybridization using Au nanoparticle modified DNA as one probe on TiO2 substrate, in which the TiO2 substrate was used not only as DNA anchors but also as the signal transducers. Hybridization between the probe and the target DNA oligonucleotides was confirmed by the decreased photocurrent of the TiO2 electrode. Compared with non-label probe, Au nanoparticles enhanced the photocurrent shifts after the hybridization. The photocurrent decreased with increasing the concentration of target DNA, indicating that this method could be used for quantitative measurements, and the discrimination of the complementary from mismatched DNA. Furthermore, the hybridization binding constant was obtained and photocurrent generation mechanism was discussed. The major advantages of this photochemical method are speed, simplicity and excellent specificity. This method provides a platform for studying a wide variety of biological processes using photoelectrochemical method.
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paper_title: Successively amplified electrochemical immunoassay based on biocatalytic deposition of silver nanoparticles and silver enhancement

paper_content:

A successively signal-amplified electrochemical immunoassay has been reported on the basis of the biocatalytic deposition of silver nanoparticles with their subsequent enlargement by nanoparticle-promoted catalytic precipitation of silver from the silver-enhancer solution. The immunoassay was carried out based on a heterogeneous sandwich procedure using polystyrene microwells to immobilize antibody. After all the processes comprising the formation of immunocomplex, biocatalytic deposition of silver nanoparticles and following silver enhancement were completed, the silver on polystyrene microwells was dissolved and quantified by anodic stripping voltammetry (ASV). The effect of relevant experimental conditions, including the concentration of ascorbic acid 2-phosphate (AA-p) substrate and Ag(I) ions, the biocatalytic deposition time, and of crucial importance, the silver enhancement time, were investigated and optimized. The anodic stripping peak current was proportional to the concentration of human IgG in a dynamic range of 0.1-10 ng ml(-1) with a detection limit of 0.03 ng ml(-1). Scanning electron microscope (SEM) was applied to characterize the silver nanoparticles before and after silver enhancement on the surface of polystyrene microplates. By coupling the highly catalytic effect of enzyme and nanoparticles to successively amplify the analytical signal, the sensitivity of immunoassay was enhanced so dramatically that this approach would be a promising strategy to achieve a lower detection limit for bioassays. (c) 2007 Elsevier B.V. All rights reserved.
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paper_title: Fabrication and photochromic study of titanate nanotubes loaded with silver nanoparticles

paper_content:

Abstract Pure anatase-TiO 2 and/or titanate nanotubes, photochromic Ag loaded titanium dioxide nanotubes (TNTs) and AgCl loaded titanate nanotubes were synthesized by hydrothermal method. The pH value during the neutralization process plays a crucial role in controlling the morphology and composition of the nanotubes. All these nanotubes were confirmed by XRD, TEM, EDS and XPS analysis. Most of them have open ends with inner/outer diameters of 7/10 nm and several hundred nanometers in length. For photochromic behavior in the case of AgCl–titanate nanotubes, the red color can be clearly observed after irradiation by red light, while the yellow, green, blue ones displayed pale black after the corresponding irradiation. On the other hand, Ag loaded TNT sample exhibited multicolor photochromism corresponding to that of incident light. The photoreduction of silver halide to Ag particle in the case of loaded AgCl particles and a particle-plasmon-assisted electron transfer from Ag nanoparticles to TiO 2 in the case of loaded Ag particles are considered to be responsible for this different behavior.
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paper_title: Silica-nanoparticle-based interface for the enhanced immobilization and sequence-specific detection of DNA

paper_content:

A biocompatible and uniform interface based on silica nanoparticles derivatized with amino groups has been constructed for the effective immobilization and sensitive sequence-specific detection of calf thymus DNA. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) results showed that a monolayer of silica nanoparticles can be formed on a gold electrode under our experimental conditions using cysteine self-assembly monolayer as binder medium. Electrochemical impedance spectroscopy and X-ray photoelectron spectroscopy (XPS) verified the successful immobilization of DNA on silica-nanoparticle-modified gold electrodes. Quantitative results demonstrated that enhanced immobilization of single-strand DNA (ss-DNA) up to 1.6×10−8 mol cm−2 could be achieved owing to the larger surface area and the special properties of silica nanoparticles. In addition, hybridization experiments demonstrated that the immobilized ss-DNA on silica nanoparticles could specifically interact with complementary DNA in solutions.
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paper_title: On-chip chemiluminescent signal enhancement using nanostructured gold-modified carbon microarrays.

paper_content:

An original method for the enhancement of chemiluminescent (CL) on-chip detection of protein and oligonucleotides is presented. This enhancement is based on the electrodeposition of a gold nanostructured layer onto a screen-printed (SP) carbon microarray prior to the immobilization of biomolecules through a well-established diazonium adduct electrodeposition. Morphological studies of the Au layer (optical and atomic force microscopy) show that the metal film is composed of nanostructured 800 nm diameter particles covering the entire graphite surface and yielding a high surface area. Using these modified SP microarrays, enhancement factors of 229 and 126 were obtained for prostate-specific antigen (PSA) and p53 oligonucleotide detection, respectively. These enhancements were associated with three different phenomena: an enhancement of the catalyzed chemiluminescent reaction by the gold surface, an increase of the specific surface area for immobilization of the probe biomolecules, and an opposite quenching...
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paper_title: The enhancement effect of gold nanoparticles as a surface modifier on DNA sensor sensitivity.

paper_content:

The enhancement of a single strain DNA probe linked to the sensor surface is of crucial importance in DNA molecule recognition. By means of nanogold modification of the sensor surface in addition to the nanogold amplifier, DNA detection sensitivity higher than 10(-16)mol/L was obtained in a Quartz Crystal microbalance (QCM) system, much higher than the ordinary QCM sensor without surface modification by nanogold.
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paper_title: Aptamer-based Au nanoparticles-enhanced surface plasmon resonance detection of small molecules.

paper_content:

Small molecules are difficult to detect by conventional SPR technique directly because the changes in the refractive index resulting from the binding processes of small biomolecules are often small. In order to extend the application of SPR biosensor in detecting a small molecule, we combine the advantage of aptamer technique with the amplifying effect of Au nanoparticles to design a sensitive SPR sensor for detecting small molecules. The principle of this sensor is based on surface inhibition detection. The aptamer is first immobilized on SPR gold film with its ss-DNA structure. The aptamer possessing this structure can be hybridized with Au nanoparticles-tagged complementary ss-DNA and result in a large change of SPR signal. However, the aptamer will change its structure from ss-DNA to tertiary structure after adenosine is added to the SPR cell. The aptamer possessing tertiary structure could not hybridize with Au nanoparticles-tagged complementary ss-DNA. Thus, the change of SPR signal resulted in the hybridization reaction between aptamer and Au nanoparticles-tagged complementary ss-DNA will decrease with the increase of the number of aptamers possessing tertiary structure, which is proportional to the concentration of the small molecule. Based on this principle, we choose a simple system (antiadenosine aptamer/adenosine) to detect the sensing ability of this SPR biosensor for a small molecule. The experimental results confirm that the SPR sensor we developed possesses a good sensitivity and a high selectivity for adenosine. The detection range for adenosine is from 1 x 10 (-9) to 1 x 10 (-6) M. More significantly, it is fairly easy to generalize this strategy to detect a spectrum of small molecules by SPR spectroscopy using different aptamers. Therefore, it is expected that this method may offer a new direction in designing high-performance SPR biosensors for sensitive and selective detection of a wide spectrum of small molecules.
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paper_title: Oligonucleotide-displaced organic monolayer-protected silver nanoparticles and enhanced luminescence of their salted aggregates.

paper_content:

N-(2-mercaptopropionyl)glycine (tiopronin) monolayer-protected silver particles were partially displaced by single-stranded oligonucleotides through ligand exchanges. The oligonucleotide-displaced particles could be hybridized with complementary fluorophore-labeled oligonucleotides. Both the oligonucleotide-displaced and hybridized particles could be aggregated by electrostatic interactions with salt in buffer solution, and the aggregates displayed enhanced luminescence from fluorophores. This result suggests the possible application of surface-enhanced fluorescence from metallic nanoparticle aggregation for DNA detection.
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paper_title: Enhanced Electrochemical Detection of DNA Hybridization Based on Au/MWCNTs Nanocomposites

paper_content:

Abstract The nanocomposites of gold nanoparticles and multi‐walled carbon nanotubes (MWCNTs) have been applied in the enhanced electrochemical detection of DNA hybridization. Gold nanoparticles coated on MWCNTs uniformly were synthesized by simply one step reaction. Target DNA was detected by the peak current difference of differential pulse voltammetry (DPV) signals of the electroactive indicator methylene blue (MB) before and after hybridization on the Au/MWCNTs modified glass carbon electrode (GCE). Due to the excellent electrical conductivity of the novel matrix, the biosensor revealed high sensitivity with the detection level down to 1.0 pM. Excellently selectivity and reproducibility were also discussed.
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paper_title: Direct DNA hybridization at disposable graphite electrodes modified with carbon nanotubes

paper_content:

The performance of glassy carbon (GCE) and graphite pencil electrodes (PGE) modified with multiwalled carbon nanotubes (CNTs) are compared, based on the direct electrochemical detection of nucleic acids. This is accomplished by monitoring the differential pulse voltammetry changes of the guanine signal. CNT-modified PGE compares favorably to that of the commonly used CNT-modified GCE owing to the intrinsic improved performance of the supporting PGE. The better intrinsic characteristics of the PGE are related to its composite structure and higher level of porosity compared to GCE. The performance characteristics of the direct DNA hybridization on the disposable CNT-modified PGE are studied in terms of optimum analytical conditions such as probe concentration, target concentration, hybridization time, and selectivity. The new DNA biosensor described here has shown some important advantages such being inexpensive, sensitive, selective, and able to generate reproducible results using a simple and direct elect...
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paper_title: Carbon nanotube-enhanced DNA biosensor for DNA hybridization detection using rutin-Mn as electrochemical indicator

paper_content:

Abstract The manganese complex of rutin(R) C 54 H 58 MnO 32 (abbreviated by MnR 2 ) was synthesized and characterized by elemental analysis and IR spectroscopy. Cyclic voltammetry (CV) and fluorescence spectroscopy were used to investigate the interaction of MnR 2 with salmon sperm DNA. It was revealed that MnR 2 presented an excellent electrochemical activity on glassy carbon electrode (GCE) and could intercalate into the double helix of double-stranded DNA (dsDNA). A novel and sensitive electrochemical DNA biosensor based on multi-walled carbon nanotubes functionalized with a carboxylic acid group (MWCNTs–COOH) for covalent DNA immobilization and enhanced hybridization detection was described. The MWCNTs–COOH modified glassy carbon electrode was fabricated and oligonucleotides with the 5′-amino group were covalently bonded to the carboxyl group of carbon nanotubes. Compared with DNA sensors with oligonucleotides directly incorporated on glassy carbon electrodes, this carbon nanotube-based assay with its large surface area and good charge-transport characteristics dramatically increased DNA attachment quantity and complementary ssDNA detection sensitivity. The target ssDNA could be quantified ranged from 1.60 × 10 −9 M to 4.80 × 10 −8 M with good linearity ( r = 0.9898) and a detection limit of 3.81 × 10 −11 M (3 σ , n = 7) was achieved by the constructed electrochemical DNA biosensor.
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paper_title: Ultrasensitive electrical biosensing of proteins and DNA: carbon-nanotube derived amplification of the recognition and transduction events.

paper_content:

A new strategy for dramatically amplifying enzyme-linked electrical detection of proteins and DNA using carbon nanotubes (CNTs) for carrying numerous enzyme tracers and accumulating the enzymatically liberated product on CNT-modified transducer is described. Such a CNT-derived double-step amplification pathway (of both the recognition and transduction events) allows the detection of DNA and proteins down to 1.3 and 160 zmol, respectively, in 25-50 muL samples and indicates great promise for PCR-free DNA analysis. The new protocol is illustrated for monitoring sandwich hybridization and antibody-antigen interactions in connection with alkaline-phosphatase tracers. The DNA-linking of CNTs and particles holds promise also for assembling hybrid nanostructures relevant to molecular electronic devices.
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paper_title: Adsorption and electrooxidation of nucleic acids at carbon nanotubes paste electrodes

paper_content:

Abstract Carbon nanotubes paste electrodes (CNTPE) are shown to be suitable for adsorptive stripping potentiometric measurements of trace levels of nucleic acids. The influence of surface pretreatments, paste composition, nature of the nucleic acid, and accumulation conditions on the adsorption and further electrooxidation of different oligonucleotides and polynucleotides at CNTPE is described. The electroactivity inherent to carbon nanotubes has allowed us to obtain a large enhancement of the guanine oxidation signal compared to that obtained at its analogue carbon (graphite) paste electrode (CPE). Trace (μg/l) levels of the oligonucleotides and polynucleotides can be readily detected following short accumulation periods with detection limits of 2.0 μg/l for a 21 bases oligonucleotide and 170 μg/l for calf thymus dsDNA. The interaction between nucleic acids and CNTPE demonstrated to be mainly hydrophobic. The confined DNA layers demonstrated to be stable in air, in 0.200 M acetate buffer pH 5.00 and in 0.020 M phosphate buffer pH 7.40 + 0.50 M NaCl.
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paper_title: Synergistic effects of nano-ZnO/multi-walled carbon nanotubes/chitosan nanocomposite membrane for the sensitive detection of sequence-specific of PAT gene and PCR amplification of NOS gene

paper_content:

Abstract The remarkable synergistic effects of the zinc oxide (ZnO) nanoparticles and multi-walled carbon nanotubes (MWNTs) were developed for the ssDNA probe immobilization and fabrication of the electrochemical DNA biosensor. The ZnO/MWNTs/chitosan nanocomposite membrane-modified glassy carbon electrode (ZnO/MWNTs/CHIT/GCE) was fabricated and the ssDNA probes were immobilized on the modified electrode surface. The preparation method is quite simple and inexpensive. The hybridization events were monitored by differential pulse voltammetry (DPV) using methylene blue (MB) as an indicator. As compared with previous MWNTs-based DNA biosensors, this composite matrix combined the attractive biocompatibility of ZnO nanoparticles with the excellent electron-transfer ability of MWNTs and fine membrane-forming ability of CHIT increased the DNA attachment quantity and complementary DNA detection sensitivity. The approach described here can effectively discriminate complementary DNA sequence, noncomplementary sequence, single-base mismatched sequence and double-base mismatched sequence related to phosphinothricin acetyltransferase (PAT) gene in transgenic corn. Under optimal conditions, the dynamic detection range of the sensor to PAT gene complementary target sequence was from 1.0 × 10 −11 to 1.0 × 10 −6 mol/L with the detection limit of 2.8 × 10 −12 mol/L. The polymerase chain reaction (PCR) amplification of nopaline synthase (NOS) gene from the real sample of one kind of transgenic soybeans was also satisfactorily detected with this electrochemical DNA biosensor, suggesting that the ZnO/MWNTs/CHIT nanocomposite hold great promises for sensitive electrochemical biosensor applications.
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paper_title: Enhancement of target-DNA hybridization efficiency by pre-hybridization on sequence-orientated micro-arrayed probes

paper_content:

Abstract The enhancement of hybridization efficiency of deoxyribonucleic acid (DNA) targets using oligonucleotide pre-hybridization is studied on two sequence-inversed micro-arrayed probes. The sequences for pre-hybridizing both oligo and target DNA are designed to be fully complementary with their shared DNA probe in a coaxial stacking configuration; i.e. they hybridize immediately alongside each other along the continuous complement probe strand. The pre-hybridizing oligo and target DNA are differentiated by being labeled with two distinct fluorescent dyes, and the cooperative effect on hybridization efficiency is investigated through the comparison of the stacking and individual hybridization configurations based on the detection signals of the labeling dyes. The results show that the pre-hybridization of a DNA oligo enhances the subsequent hybridization efficiency of the target-DNA coupling onto the same probe. The efficiency is enhanced if the hybridization position occurs at a site close to the substrate surface.
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paper_title: Enzyme enhanced quantitative determination of multiple DNA targets based on capillary electrophoresis.

paper_content:

In the current paper, enzyme enhanced simultaneous quantitative determination of multiple DNA targets based on capillary electrophoresis (CE) was described. We used three biotin-modified DNA probes, which reacted with avidin-conjugated horseradish peroxidase (avidin-HRP) conjugate to obtain the HRP labeled probes, to hybridize with three corresponding targets. The resulting mixture containing double-strand DNA (dsDNA)-HRP, excess single-strand DNA (ssDNA)-HRP and remaining avidin-HRP was separated by capillary electrophoresis, and then the system of HRP catalyzing H(2)O(2)/o-aminophenol (OAP) reaction was adopted. The catalytic product was detected with electrochemical detection. With this protocol, the limits of quantification for the hybridization assay of 21-, 39- and 80-mer DNA fragments were of 1.2 x 10(-11), 2.4 x 10(-11) and 3.0 x 10(-11)M, respectively. The multiplex assay also provided good specificity without any cross-reaction.
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paper_title: Enhancement of DNA micro-array analysis using a shear-driven micro-channel flow system.

paper_content:

A very simple micro-channel flow system is used to investigate the potential gain in hybridization rate stemming from the induction of a convective flow past the surface of a DNA micro-array. Reporting on a series of preliminary experiments wherein a two-dimensional convective flow is created past the surface of a conventional micro-array slide, the analysis time could be brought down from overnight waiting (16 h) to some 10 to 30 min. The experiments open the road towards the development of novel, convection-driven hybridization systems yielding shorter analysis times, and/or lower detection limits.
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paper_title: Label-free DNA sequence detection with enhanced sensitivity and selectivity using cationic conjugated polymers and PicoGreen.

paper_content:

In this Letter, we demonstrate that PicoGreen can be used in combination with cationic conjugated polymers to develop label-free DNA sensors with enhanced detection efficiency and further improved selectivity. The high selectivity enables detection of single nucleotide mismatch even at room temperature. This method uses all commercially available materials. It is low cost, is simple to use, and works in a "mix-and-detect" manner. The detection sensitivity could be improved by a factor of 19 times through resonance energy transfer using poly[(9,9-di(3,3'-N,N'-trimethyl-ammonium)propylfluorenyl-2,7-diyl)-alt-co-(1,4-phenylene)] diiodide salt (PFP) as a light harvesting complex, to take advantage of its collective optical response and optical amplification effects. The further improved selectivity is ascribed to the stronger binding interaction between PicoGreen with dsDNA compared to that between PicoGreen and ssDNA, which results in selective repelling of PicoGreen away from the DNA strands.
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paper_title: A novel approach for the detection of DNA using immobilized peptide nucleic acid (PNA) probes and signal enhancement by real-time immuno-polymerase chain reaction (RT-iPCR)

paper_content:

A new approach for the detection of DNA target molecules is described, using capture probes and subsequent signal enhancement by a uniform polymerase chain reaction (PCR). Peptide nucleic acid probes were immobilized in real-time PCR-compatible microtiter plates. After hybridization of biotinylated DNA targets, detection was performed by real-time immuno-PCR, a method formerly used for protein detection. We demonstrate the feasibility of this strategy for the qualitative detection of DNA oligonucleotides with a detection limit (LOD) of 6 attomol. Furthermore, the method was applied to PCR-amplified samples from genetically modified maize DNA (Mon810). A 483-bp DNA fragment was detected in mixture with 99.9% of noncomplementary DNA with a sensitivity down to the level of attomole.
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paper_title: Electrochemical DNA sensors based on enzyme dendritic architectures: an approach for enhanced sensitivity

paper_content:

The modification of enzymes with multiple single-stranded oligonucleotides opens up a new concept for the development of DNA sensors with enhanced sensitivity. This work describes the generation of reporter sequences labeled with an enzyme for the demonstration of their ability to specifically hybridize and to permit signal amplification by successive hybridization steps. The synthetic pathway for the labeling of GOx with oligonucleotide sequences is based on the oxidation of the glycosidic residues of the enzyme and their covalent binding with 5‘-end amine-modified oligonucleotides. Spectrophotometric characterization of these functionalized sequences results in an average number of three linked oligonucleotides per enzyme molecule. Their specificity is demonstrated in both a direct and a sandwich-type hybridization assay. The transduction of the enzyme-linked DNA sensors is based on self-assembled multilayers, including a chemically modified anionic horseradish peroxidase electrochemically connected to ...
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paper_title: Hybridization Enhancement Using Microfluidic Planetary Centrifugal Mixing

paper_content:

DNA microarrays produce their greatest sensitivities when hybridized using concentrated samples and effective mixing; however, these goals have proved elusive to combine. If samples are diluted enough to fill larger chambers, then mixing works well using either pumping or gravity with rotation, although sensitivities will suffer. Various techniques for mixing concentrated samples in small thin chambers have been proposed; however, they often leave streaks or scars, and their reusable components require careful cleaning. Here we introduce a versatile new microfluidics platform, a two-axis centrifuge whose fluidic chambers rotate in a planetary relationship to a radial gravitational field. This paradigm readily overcomes surface and viscous forces even in chambers only 50 μm thin. Thin chambers obviate the need for sample dilution and increase sensitivities and dynamic ranges 10-fold. In comparisons against conventional mixing using the same 10 μg of starting total RNA on 22 000-probe arrays, 10 000 more us...
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paper_title: Label-Free “Digital Detection” of Single-Molecule DNA Hybridization with a Single Electron Transistor

paper_content:

Here we present a novel assay that eliminates fluorescent labels and enables “digital detection” of single-molecule DNA hybridization in complex matrixes with greatly simplified protocols. Electronic coupling of the binding state of a single oligonucleotide to the quantum dot (QD) of a single electron transistor (SET) affords direct observation of binding events in real-time via “molecular gating”. The change of electrostatic charge associated with the molecular capture is used in lieu of a gate electrode to modulate the SET conductivity. Target oligos containing base mismatches do not elicit SET response under 0.1X SSC at room temperature nor do changes in ionic strength or pH. Furthermore, hybridization is detected even in optically inaccessible matrixes such as serum or quanidinium thiocyanate lysis buffer.
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paper_title: Enhanced reactivity of amino-modified oligonucleotides by insertion of aromatic residue

paper_content:

We developed novel amino-modifying reagents, of which an amino group was connected with an aromatic residue by aliphatic linker. It was proved that the insertion of the aromatic residue could increase the reactivity of the amino group on oligonucleotides in comparison with conventional amino-modification.
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Title: Nanomaterial-Assisted Signal Enhancement of Hybridization for DNA Biosensors: A Review

Section 1: Introduction
Description 1: Provide an overview of DNA importance, traditional DNA biosensors, the necessity for signal enhancement, and the role of nanomaterials in this context.

Section 2: DNA Hybridization and Signal-Detecting Methods
Description 2: Explain the concept of DNA hybridization, various detection methods, and the significance of electrochemical methods in DNA detection.

Section 3: Nanosemiconductors
Description 3: Discuss the use of nanosemiconductors, specifically ZnO and SnO2, for signal enhancement in DNA biosensors, including specific studies and findings.

Section 4: Quantum-dots (QDs)
Description 4: Review the application of QDs for fluorescence-based DNA detection, highlighting their unique properties and recent advances in QD-assisted DNA biosensors.

Section 5: Nanoparticles (NPs)
Description 5: Examine the role of nanoparticles, particularly Au and Ag NPs, in enhancing DNA biosensor signals, along with relevant research and methods used.

Section 6: Carbon Nanotubes (CNTs) and their Composites
Description 6: Explore the utilization of CNTs and their composites in DNA biosensors, including their electronic properties, signal enhancement strategies, and related research findings.

Section 7: Signal Enhancement of DNA Biosensor Based on Non-Nanomaterials for Comparison
Description 7: Compare nanomaterial-assisted signal enhancement strategies with non-nanomaterial methods, including biochemical approaches and enzyme-based amplification.

Section 8: Conclusions and Perspectives
Description 8: Summarize the review, highlighting the key findings and potential future directions for nanomaterial-assisted signal enhancement in DNA biosensors.