2012 Student Research Conference:
25th Annual Student Research Conference

Natural Bond Orbital Analysis to Rationalize Stability of the Transfer RNA Anticodon
Rachel N. Witts
Dr. Maria Nagan and Dr. Eric V. Patterson, Faculty Mentors

Transfer RNA (tRNA) plays an essential role in the process of manufacturing proteins. Specifically, the anticodon stem loop (ASL) region of tRNA is the portion that is coded for by messenger RNA (mRNA) to carry the proper amino acid to the growing polypeptide chain. The anticodon, positions 34-36 of the tRNA strand, exhibits a stair-stepped conformation of its bases. Modified bases, thought to increase the stability of the stacking interaction, occur naturally in positions 34 and 37. The interactions within the anticodon were studied using quantum mechanical calculations, specifically the M06-2X level of theory with the 6-31+G(d,p) basis set and natural bond orbital (NBO) theory. In addition, these calculations were performed with solvation effects taken into account by the use of the SMD solvation model. This study provided insight into the interactions that stabilize the anticodon as well as the roles played by the modified bases in the 37th position.

Keywords: Transfer RNA, Anticodon, Natural Bond Orbital analysis, Density functional theory, solvation, modified bases


Presentation Type: Oral Paper

Session: 310-1
Location: MG 2090
Time: 1:00

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