Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.

ABSTRACT: Molecular mechanics with all-atom models was used to understand the conformational preference of tandem guanine-adenine (GA) noncanonical pairs in RNA. These tandem GA pairs play important roles in determining stability, flexibility, and structural dynamics of RNA tertiary structures. Previous solution structures showed that these tandem GA pairs adopt either imino (cis Watson-Crick/Watson-Crick A-G) or sheared (trans Hoogsteen/sugar edge A-G) conformations depending on the sequence and orientation of the adjacent closing base pairs. The solution structures (GCGGACGC)₂ [Biochemistry, 1996, 35, 9677-9689] and (GCGGAUGC)₂ [Biochemistry, 2007, 46, 1511-1522] demonstrate imino and sheared conformations for the two central GA pairs

SUBMITTER: Aytenfisu AH 

PROVIDER: S-EPMC3985902 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature