Revised theory on DNA renaturation kinetics and its experimental verification

Many molecular biology and genomics techniques (including C(0)t analysis, PCR, and HPLC) depend upon the renaturation of DNA in solution. Traditionally, the renaturation process has been treated as a second-order kinetics reaction with the concentration of the DNA as the order parameter. However, second-order kinetics only describes complementary strand recognition and not the intramolecular "zipping" of complementary strands once recognition has been established. And also we cannot use simply the DNA concentration as the order parameter. Here I present an improved model that takes both phenomena into account using "mol-bases" as the order parameter. The model was tested experimentally and found to provide a more accurate description of the observed data than previous DNA renaturation models based solely on second-order kinetics.