Positional and neighboring base pair effects on the thermodynamic stability of RNA single mismatches.

ABSTRACT: Many naturally occurring RNA structures contain single mismatches, many of which occur near the ends of helices. However, previous thermodynamic studies have focused their efforts on thermodynamically characterizing centrally placed single mismatches. Additionally, algorithms currently used to predict secondary structure from sequence are based on two assumptions for predicting the stability of RNA duplexes containing this motif. It has been assumed that the thermodynamic contribution of small RNA motifs is independent of both its position in the duplex and the identity of the non-nearest neighbors. Thermodynamically characterizing single mismatches three nucleotides from both the 3' and 5' ends (i.e., off-center) of an RNA duplex and comparing these results to those of the same single mis

SUBMITTER: Davis AR 

PROVIDER: S-EPMC2991393 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature