30th Annual Student Research Conference
Investigation of Mismatch Base Pairing in DNA Polymerase I
Andrew V. Yeager
Dr. Bill R. Miller, Faculty Mentor
DNA polymerase is the primary enzyme responsible for DNA replication in living organisms. The high fidelity of DNA polymerase for Watson-Crick nucleotide pairs complicates investigation of nucleotide mismatches using traditional experimental methods. Modern computational methods allow for study of such mismatches at the atomic level. All mismatch template-dNTP combinations were in silico mutated into the active sites of three known crystal structures of DNA polymerase, each conformation representing a different stage in nucleotide addition. The molecular dynamics software package AMBER then propagated simulations over one μs for each template-dNTP combination. Each simulation was then visualized using Visual Molecular Dynamics (VMD) and analyzed using a number of AMBER-associated and in-house programs, including binding affinity analysis and characterization of the activity of DNA polymerase. Simulations and the results of analysis will be discussed.
Keywords: DNA Polymerase, Molecular Dynamics
Topic(s):Chemistry
Biology
Computer Science
Presentation Type: Oral Paper
Session: 103-2
Location: MG 1096
Time: 8:15