Effect of primer binding probability on amplified misprimed DNA by means of a computational study on the polymerase chain reaction

Abstract

Amplification of deoxyribonucleic acid (DNA) fragments by the polymerase chain reaction (PCR) has significantly contributed to the rapid development of the modern biomedical sciences. Amplification of DNA fragments is essential in order to obtain large quantities of particular segmentts) in a gene to perform experiments and analyses. Certain parameters affect the ideal amplification of DNA and one of them is misprimed synthesis. An investigation was conducted to determine whether the amplified DNA that are formed due to misprimed synthesis, i.e., the DNA that are not of interest, are due to the variation in the probability values of primer binding for increasing cycles in the presence of multiple binding sites. First, background information on genetics is provided along with an introduction to modeling biological systems. Second, the previous work on modeling the PCR by various authors including the similarity and dissimilarity with the proposed work are discussed briefly. Third, the procedure of the developed model, computational and mathematical parts of the model, is discussed with an overview of enzyme kinetics. Fourth, the results are analyzed and the findings and discussion on the Interpreted results is provided. Plots involving the critical parameters are provided and the effects discussed. Finally, the conclusions are presented. It is noted that there was effect of the primer binding probability on the production of amplified DNA of interest in the presence of multiple binding sites. There was a significant effect on the yield and a significant purity. Future scope of the developed model is also elicited.