Mark West
Principal Mechanical
Engineer Design Continuum Boston, Mass.

Trilogy single-molecule analyzers from U.S. Genomics can analyze 500 DNA samples in a single 8-hr shift.

Boston-based Design Continuum recently delivered five Trilogy singlemolecule analyzers to U.S. Genomics of Woburn, Mass. The machines take DNA from humans, plants, or animals and tell if a particular gene is present in a sample. The new machines improve on their predecessors by increasing throughput from 50 to 500 samples in an 8-hr shift, roughly a sample/min. This decreases the cost/test and speeds research into diseases, letting them analyze single molecules of DNA, RNA, and proteins.

Samples are in 10 m l of solution in a standard 96-well plate. Each well contains a DNA sample and some chemistry to identify if a particular gene is present. The instrument is basically a laserbased optical scanner. A laser shines onto the sample and reads the results of the chemical reaction, analyzing the refraction from the sample.

Engineers designed a sample delivery system that makes it easier for researchers to place samples into the machine. Once the samples are in place, computer controls automatically move them precisely through the analysis process. The sample delivery system is carefully calibrated with the optical systems to provide precision analysis and maximum sample throughput.

The first generation of laser-based analyzers were chip-based systems. Samples were placed in a microfluidic chip which was inserted in the machine where the optics would read the sample as it flowed through the chip. This required loading and unloading chips. It also meant samples had to be positioned to an accuracy of 1 micron under the optics. The analyzers used stepper motors that were microstepped and high-precision crossed roller-bearing stages with fine-pitch ball screws and linear encoders on the axes to attain submicron resolution

The probe draws samples from each of the 96 wells for analysis and can move between one well and any other in less than 1 sec.


Second-generation analyzers use a 96-well plate that loads 96 samples at once. Instead of using microchannels in the chip, the microchannel is a permanent part of the machine. So the machine accesses each of the 96 wells and draws the sample through the microchannel eliminating the need to align the optics to submicron accuracy. There is still submicron accuracy in the microchannel, but it's manually done once. Consequently, the new analyzers use stepper motors which are half-stepped, not microstepped. There are no linear encoders and no ball screws, only leadscrews.

Another requirement was that the scanning head must get from any well to any other well in less than a second. A longer leadscrew handles the speed requirement. On the first machine, the lead was 1 mm. On the new one, it's 10 mm for greater linear acceleration and speed.

Because of the high-magnification optics, prototypes were affected by external vibration from nearby trucks and freight trains. This required building in vibration control to stabilize the optics and aligning them by folding the five laser beams in each machine with a series of mirrors. The design team examined both active and passive ways to eliminate vibration, including systems with tables floating on air. They decided to use a pendulum vibrationisolation system. The chassis' main mode of vibration was horizontal. Suspending the optic system with a pendulum arrangement eliminates the horizontal vibration to the head or the optics. The mechanical structure has a natural frequency of 50 Hz and the pendulum system is 1 Hz.

Early and late-generation machines used a Galil motion controller. The first generation used a PCI card inside the computer, so the whole machine was computer controlled. On the second generation, a stand-alone controller card has the stepper motor drivers on it. All of this is housed in 19-in. rack mounts in the bottom of the machine.