Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations.

ABSTRACT: Hairpin loops belong to the most important structural motifs in folded nucleic acids. The d(GNA) sequence in DNA can form very stable trinucleotide hairpin loops depending, however, strongly on the closing base pair. Replica-exchange molecular dynamics (REMD) were employed to study hairpin folding of two DNA sequences, d(gcGCAgc) and d(cgGCAcg), with the same central loop motif but different closing base pairs starting from single-stranded structures. In both cases, conformations of the most populated conformational cluster at the lowest temperature showed close agreement with available experimental structures. For the loop sequence with the less stable G:C closing base pair, an alternative loop topology accumulated as second most populated conformational state indicating a possible loop s

SUBMITTER: Kannan S 

PROVIDER: S-EPMC3201870 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature