2007 Student Research Conference:
20th Annual Student Research Conference


Molecular Dynamics Simulations of E. coli tRNAPhe
Bryan D. Sitzmann
Dr. Maria Nagan, Faculty Mentor

Modifications of the four primary nitrogenous bases are quite common in ribonucleic acid (RNA) molecules and occur in all organisms. Escherichia coli tRNAPhe requires two modified bases, 2-thiomethyl-N6-dimethylallyl adenosine (ms2i6A) and pseudouridine for accurate translation of the genetic code. Nikonowicz and coworkers have shown by NMR spectroscopy that ms2i6A, in conjunction with metal ions, stabilizes the anticodon loop, possibly into a U-turn motif. However, the exact structure of the fully modified anticodon loop and the influence of metal ions has not been determined. Molecular dynamics studies of E. coli tRNAPhe in solution examining the effect of modified bases and Mg2+ on the anticodon loop are presented. Cobalt(III) hexamine is used to mimic hydrated Mg2+ found in vivo. These studies will provide a better understanding of how nucleic acid base modifications affect tRNA structure and therefore accurate translation.

Keywords: Molecular Dynamics, RNA, modified base, E. coli, ms2i6A, pseudouridine, cobalt(III) hexamine


Presentation Type: Oral Paper

Session: 12-3
Location: VH 1212
Time: 8:45 am

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