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

杜鲁门州立大学的Eric Patterson和Maria Nagan获得了理论与计算化学项目的本科院校研究奖，该项目的研究涉及轨道相互作用的量子力学研究，这些轨道相互作用负责塑造几种转移核糖核酸（tRNA）结构中发现的反密码子茎环（ASL）的阶梯状区域。反密码子堆积的三个相关项目正在探索中，以了解（1）序列特异性对阶梯构象的影响，（2）动力学对轨道相互作用能的影响，在一组平行采样的人类tRNALys中，3结构和（3）位于反密码子正上方的非标准核酸碱基在稳定反密码子中的作用。影响这种独特结构特征的重要立体电子因素正在使用密度泛函理论（DFT）在M05-2X/6-31+G（d，p）理论水平结合详细的自然键轨道（NBO）分析进行鉴定。由于mRNA对tRNA的识别对于将遗传密码正确翻译成蛋白质至关重要，因此这项工作将揭示生命系统健康运作的关键过程。 这项工作是在一个以本科生为主的机构进行的，并通过专门关注本科生而产生更广泛的影响，其中一些人是代表性不足的少数民族。 PI具有与本科生合作和指导本科生的重要经验。 co-PI Nagan是NSF资助的MERCURY联盟的一部分，因此该项目的学生也参加了MERCURY赞助的活动。

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.