2008 Student Research Conference:
21st Annual Student Research Conference

Molecular Orbital Interactions in the Anticodon of Transfer RNA
Elizabeth E. Koballa* and Nick H. Hopkins
Dr. Maria Nagan and Dr. Eric V. Patterson, Faculty Mentors

Accurate recognition of messenger ribonucleic acid (mRNA) by various transfer RNA (tRNA) molecules is essential to protein synthesis. Precise positioning of anticodon nitrogenous bases in line with the cognate mRNA codon is required for correct amino acid incorporation into the polypeptide chain. This study identifies the molecular orbitals stabilizing the three nitrogenous bases of the tRNA anticodon into a stair-stepped conformation. Interestingly, there is no overt surface area overlap between bases; stabilizing forces in this unique structure are unknown. The effect of naturally occurring modified bases at the position directly above the anticodon (the 37th position) on crystal structure stabilization is also examined. Anticodon base structures were obtained from experimentally determined tRNA structures and truncated to the anticodon. Hydrogens were added to the crystal structures and geometry optimizations were performed to determine minimum energy hydrogen positions. Natural bond orbital interactions between orbitals of separate nitrogenous bases were identified and analyzed.

Keywords: RNA, molecular orbital, anticodon, tRNA, base stacking, nitrogenous bases


Presentation Type: Oral Paper

Session: 44-3
Location: VH 1320
Time: 3:15

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