29th Annual Student Research Conference
Investigation of Guanine-Nucleotide Base Pairing in DNA Polymerase
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. Guanine was placed on the template DNA strand and paired with nucleotide triphosphates in the active site of DNA polymerase using in silico mutations. Beginning with three known crystal structures of DNA polymerase, the molecular dynamics software package AMBER propagated simulations over one μs for each guanine-nucleotide combination in all three starting conformations. Once simulations were complete, each was visualized using Visual Molecular Dynamics (VMD) and analyzed using a number of programs associated with AMBER. Simulations and the results of analysis will be discussed.
Keywords: DNA Polymerase, Biochemistry, Computational Chemistry, Chemistry, Biology, DNA Replication
Topic(s):Chemistry
Biology
Computer Science
Presentation Type: Oral Paper
Session: -2
Location: MG 2001
Time: 9:45