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I'm a molecular bio novice, and I'm trying to understand the differences between regular PCR and RACE PCR. If it wanted to sequence my PCR product that might be hundreds, if not thousands of bps long, I should use RACE PCR correct? My goal is to sequence the active site of some enzymes I'm interested in, but I'm not sure how to go about designing PCR primers for a specific site on my protein. Additionally, the active site is over 100 amino acids long, which would imply that my PCR product has to be over 300 bps long. Regular PCR amplicons have trouble amplifying long strands of DNA correct? I was thnking about using RACE PCR to amplify my entire cDNA strand that is 4000 bps long and then just sequencing the RACE product. Would RACE work for that many bps in my cDNA?

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This is a lot of questions in one very compressed paragraph. It would probably be best if you asked separate questions. –  dd3 Mar 20 '13 at 17:55

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Judging by your post history, it seems like you may want to pick up an introductory book on molecular biology. This question is really asking a number of questions. I will attempt to answer the difference between PCR and RACE, and I would suggest asking the others as separate questions, as @dd3 has suggested.

Polymerase Chain Reaction (PCR) is the basic method of amplifying a small amount of DNA (the template) into an exponentially large amount of DNA. This method assumes the knowledge of the sequence of (at least) the regions of DNA flanking what you wish to amplify. Using these flanking sequences, two short oligonucleotides (e.g., 18-24 nucleotides), called primers, are ordered such that one primer matches the 5' strand at the start of the sequence, while the other primer matches the 3' strand at the end of the sequence. When these primers are mixed together with the template DNA, and a DNA polymerase enzyme, and subjected to specific temperature cycles, amplification occurs.

RACE PCR is a specific type of PCR. RACE (Rapid Amplification of cDNA Ends) PCR is used when the template strand to be amplified is a specific mRNA message. In other words, this form of PCR produces a DNA copy of cDNA from an mRNA starting product. The exact details of RACE depends on which type you wish to use and can be looked up elsewhere.

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