CHOOSING HIGHLY SPECIFIC PRIMERS FOR THE POLYMERASE CHAIN-REACTION USING THE OCTOMER FREQUENCY DISPARITY METHOD - APPLICATION TO CHLAMYDIA-TRACHOMATIS

The eight-nucleotide sequence (octomer) at the 3' end of PCR primers i s important to PCR specificity. We describe a correlation between the specificity of PCR primers used with human DNA and the frequency of th e 3' octomer in a human database. We therefore applied a methodology ( OFD) based on octomer frequency disparity to identify 16 PCR targets i n the chromosome of the intracellular bacterium, Chlamydia trachomatis (Ct). In addition, the 16 sets of primers were tested with a standard procedure. All the primer pairs were highly specific for Ct and did n ot lead to non-specific amplification when used with human DNA. This w ork shows that the choice of specific PCR primers is possible using a method based on the statistical representativeness of octomers in geno mes.