2006 Student Research Conference:
19th Annual Student Research Conference

Science

Molecular Dynamics Simulations of Escherichia Coli tRNAPHE
Bryan D. Sitzmann
Dr. Maria Nagan, Faculty Mentor

Modifications of the four primary nitrogenous bases are quite common in ribonucleic acid (RNA). Nonstandard nucleic acid bases occur in all organisms. Many studies are interested in determining the role of these modifications in transfer RNA (tRNA) structure and function. Escherichia coli tRNAPhe requires two modified bases, 2-thiomethyl-N6-dimethylallyl adenosine (ms2i6A) and pseudouridine for accurate translation of the genetic code. The preliminary nuclear magnetic spectroscopy (NMR) structure of the fully modified and unmodified E. coli tRNAPHE anticodon stem loop has been solved (Cabello-Villegas J. Mol. Biol. 2002, 319. 1015-1034). The purpose of this project is to observe how E. coli tRNAPHE behaves in solution with and without its modified bases. Four molecular dynamics simulations of E. coli tRNAPHE with various modified bases have been conducted. These studies will provide a better understanding of how nucleic acid base modifications affect tRNA structure and therefore accurate translation.

Keywords: tRNAPHE, modified base, E. coli, tRNA, molecular dynamics

Topic(s):Chemistry

Presentation Type: Oral Paper

Session: 53-3
Location: VH 1432
Time: 3:15

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