title: Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure.
abstract: Transfer RNA (tRNA) anticodons adopt a highly ordered 3'-stack without significant base overlap. Density functional theory at the M06-2X/6-31+G(d,p) level in combination with natural bond orbital analysis was utilized to calculate the intramolecular interactions within the tRNA anticodon that are responsible for stabilizing the stair-stepped conformation. Ten tRNA X-ray crystal structures were obtained from the PDB databank and were trimmed to include only the anticodon bases. Hydrogenic positions were added and optimized for the structures in the stair-stepped conformation. The sugar-phosphate backbone has been retained for these calculations, revealing the role it plays in RNA structural stability. It was found that electrostatic interactions between the sugar-phosphate backbone and the base provide the most stability, rather than the traditionally studied interbase stacking. Base-stacking interactions, though present, were weak and inconsistent. Aqueous solvation was found to have little effect on the intramolecular interactions.
authors.affiliation: Department of Chemistry, Truman State University, 100 East Normal, Kirksville, Missouri 63501, USA.
authors.forename: Rachel N
authors.initials: RN
authors.lastname: Witts
authors.forename: Emily C
authors.initials: EC
authors.lastname: Hopson
authors.forename: Drew E
authors.initials: DE
authors.lastname: Koballa
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Van Boening
authors.forename: Nicholas H
authors.initials: NH
authors.lastname: Hopkins
authors.forename: Eric V
authors.initials: EV
authors.lastname: Patterson
authors.forename: Maria C
authors.initials: MC
authors.lastname: Nagan
mesh_terms: D000926:Anticodon; D030562:Databases, Protein; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011789:Quantum Theory; D012343:RNA, Transfer / Q000737:chemistry*; D055672:Static Electricity
chemical_list: D000926:Anticodon; D012343:RNA, Transfer