A Molecular Dynamics Investigation of the Thermostability of DNA Polymerase

Abstract

DNA polymerase replicates DNA within organisms. Since the development of polymerase chain reactions (PCR) in the early 1980s, DNA polymerase has also become a critical tool in biotechnology. DNA polymerase I from Thermusaquaticus(TaqDNA polymerase) is an ideal prototype for PCR due to its thermostability and activity at high temperatures. However, becauseTaq DNA polymerase lacks of a functional 3′ to 5′ exonucleaseit replicates with a relatively high error rate. In addition, Taq DNA polymerase often begins DNA replication at room temperature, which results in mispriming and nonspecific products. In an effort to improve its functionality as a PCR agent,Kermechiev and colleagues (2003) performed a series of random mutationsand found than an I707L mutation reduced the activity at low temperatures. It is unclear how this structural change affects Taq DNA polymerase activity at low temperatures. Molecular Dynamic studies at high and low temperatures on wild‐type and I707L mutated Taq DNA polymerase were employed in order to better understand the structure‐function relationship in this important enzyme. Following simulation using AMBER MD Algorithm, the I707L mutated Taq DNA polymerase was more dynamic at higher temperatures.