Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides

Abstract

Results from optical melting studies of Watson-Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides are used to determine nearest neighbor thermodynamic parameters for predicting the stabilities of such duplexes. The results are consistent with the physical model assumed by the individual nearest neighbor-hydrogen bonding model, which contains terms for helix initiation, base pair stacking and base pair composition. The sequence dependence is similar to that for Watson-Crick complementary RNA/RNA duplexes, which suggests that the sequence dependence may also be similar to that for other backbones that favor A-form RNA conformations. © Copyright 2006 Oxford University Press.