On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies.

ABSTRACT: We use a combination of database analysis and quantum chemical studies to investigate the role of cis and trans Hoogsteen:Hoogsteen (H:H) base pairs and associated higher-order structures in RNA. We add three new examples to the list of previously identified base-pair combinations belonging to these families and, in addition to contextual classification and characterization of their structural and energetic features, we compare their interbase interaction energies and propensities toward participation in triplets and quartets. We find that some base pairs, which are nonplanar in their isolated minimum energy geometries, attain planarity and stability upon triplet formation. A:A H:H trans is the most frequent H:H combination in RNA structures. This base pair occurs at many distinct position

SUBMITTER: Sharma P 

PROVIDER: S-EPMC2856888 | biostudies-literature | 2010 May

REPOSITORIES: biostudies-literature