The Polymerase Chain Reaction (PCR) procedure is a major laboratory technique used in the Human Genome Project for amplification of sequence fragments. One of the difficulties encountered when using PCR is that the product can be contaminated with the DNA of nongenomic sequences, most notably mitochondrial DNA. PCR is initiated by using small sequences, usually 20 or fewer bases, that act as primers for the reaction. This work is an attempt to recognize primers to avoid, in the sense that they will cause mitochondrial DNA to amplify and contaminate the genomic DNA product. Computer programs were written that, for a given primer, first find all locations of them in human mitochondrial DNA, and then compute whether PCR amplification can be expected, based on combinations of primer locations that are known to cause amplification. In a collaboration with Dr. Steve Zullo of NIMH, we have developed a program, OLIGFIND, which finds all locations of n-mers (n = 6 to 10) in sequence data. The program has been used with mitochondrial sequences to determine the best primers for PCR of genomic sequences. Contamination of genome sequences by mitochondria during PCRing is a big problem, and this work should help prevent such contamination by identifying primer sequences that do not occur in mitochondria, or occur in a fashion that does not interfere with genomic priming. Our paper (published with six others) """"""""Competition for Nuclear DNA STS Primers by Mitochondrial DNA"""""""", will appear in the August issue of PCR Methods and Applications.
