RUI: Quantum Characterization of Stair-Stepped Base Stacking Interactions in tRNA

Truman State University, Kirksville MO

Investigators

Abstract

Eric Patterson and Maria Nagan of Truman State University are funded by a Research in Undergraduate Institutions (RUI) award from the Theoretical and Computational Chemistry program for research involving quantum-mechanical studies of the orbital interactions responsible for shaping the stair-stepped region of the anticodon stem loop (ASL) found in several transfer ribonucleic acid (tRNA) structures. Three related projects of anticodon stacking are being explored to understand (1) sequence-specific effects on the stair-stepped conformation, (2) the effects of dynamics on orbital interaction energies in a statistically-sampled set of human tRNALys,3 structures and (3) the role of nonstandard nucleic acid bases positioned directly above the anticodon in stabilizing the anticodon. Significant stereoelectronic factors that influence this unique structural feature are being identified using density functional theory (DFT) at the M05-2X/6-31+G(d,p) level of theory in conjunction with detailed natural bond orbital (NBO) analysis. Because tRNA recognition by mRNA is critical to proper translation of the genetic code into proteins, this work will shed light on a process key to the healthy functioning of living systems. The work is being carried out at a predominately undergraduate institution and is having a broader impact through its exclusive focus on undergraduate students, some of whom are under-represented minorities. The PIs have significant experience working with and mentoring undergraduates. co-PI Nagan is part of the NSF-funded MERCURY consortium so students in this project are participating in MERCURY-sponsored events as well.