Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.

ABSTRACT: Extra unmatched nucleotides (single base bulges) are common structural motifs in folded RNA molecules and can participate in RNA-ligand binding and RNA tertiary structure formation. Often these processes are associated with conformational transitions in the bulge region such as flipping out of the bulge base from an intrahelical stacked toward a looped out state. Knowledge of the flexibility of bulge structures and energetics of conformational transitions is an important prerequisite to better understand the function of this RNA motif. Molecular dynamics simulations were performed on single uridine and adenosine bulge nucleotides at the center of eight basepair RNA molecules and indicated larger flexibility of the bulge bases compared to basepaired regions. The umbrella sampling method was

SUBMITTER: Barthel A 

PROVIDER: S-EPMC1403169 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature