DNA Polymerase-primer/Template Interaction Plays An Important Role In The Efficiency Of Polymerase Chain Reaction (PCR)

PCR is developed for amplification of the DNA and RNA in vitro and it has a profound impact on modern molecular biology. Proper primer design is essential and crucial for a successful PCR. Though there are a set of parameters that common primer design programs rely on. However, it exactly ignores the influence of the interactions between DNA polymerase and primer/template DNA to primer design.Here by constructing three dimensional structure model of Taq DNA polymerase with primer/template DNA, we designed primers based on the results of binding free energies of Taq DNA polymerase and primer/template DNA with different sequences. From PCR experiment, we determines that the efficiency of PCR is indeed associated with the binding affinity of DNA polymerase with primer and binding free energy of DNA polymerase with primer/template DNA is lower, PCR assay is more effective. Together, the efficiency of primers designed based on the binding free energies is higher than the efficiency of the best primers recommended by primer design software which are widely used nowadays. Meanwhile, we used structure-based models (SBM) to simulate the conformation of Taq DNA polymerase from open form to closed form. The trajectories from the open form to closed form were obtained after simulation. And this can help us understand interactions between DNA polymerase and primer/template DNA. So we think this new discovery could facilitate to design more efficient primers for PCR.