1. Fluctuations in RMSDs (Å)
E. coli tRNAPhe Simulations with Modified Bases
Maria Nagan, Department of Chemistry, Truman State University, Kirksville, MO 63501
We are trying to understand how modified bases affect RNA structure. In E. coli tRNAPhe, two modified bases we believe in concert with Mg2+ in vivo, help the tRNA anticodon retain a canonical structure. In the absence of modified bases, the tRNAPhe base pairs all the way into the anticodon loop. With modified bases, it opens up but G34 remains dynamic. Divalent and trivalent ions are required to stabilize the structure. MD simulations with cobalt(III) hexamine examine how these ions interact with the RNA structure and determine its conformation.
tRNAPhe (ms2i6A,)
tRNAPhe with [Co(NH3)6]3+
Fluctuations in RMSDs (Å)
Standard deviations in RMSDs for individual residues indicates that G34 fluctuates more than other residues in the presence of ms2i6A37.