ArticleJournal of biosciences2007
Theoretical analysis of noncanonical base pairing interactions in RNA molecules.
Article in Journal of biosciences, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction.Interdisciplinary sciences, computational life sciences · 2022Article
- Halogen-Bonded Guanine Base Pairs, Quartets and Ribbons.International journal of molecular sciences · 2020Article
- Article
- Estimating Strengths of Individual Hydrogen Bonds in RNA Base Pairs: Toward a Consensus between Different Computational Approaches.ACS omega · 2019Article
- How Does MgBiophysical journal · 2017Article
- RNABP COGEST: a resource for investigating functional RNAs.Database : the journal of biological databases and curation · 2015Article
- Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position.Journal of molecular modeling · 2012Article
- Determination of low-energy structures of a small RNA hairpin using Monte Carlo-based techniques.Journal of biosciences · 2012Article
- Molecular electrostatic potentials of DNA base-base pairing and mispairing.Journal of molecular modeling · 2012Article
- On the role of Hoogsteen:Hoogsteen interactions in RNA: ab initio investigations of structures and energies.RNA (New York, N.Y.) · 2010Article
- MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.RNA (New York, N.Y.) · 2009Article
- Modeling the noncovalent interactions at the metabolite binding site in purine riboswitches.Journal of molecular modeling · 2009Article
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Authors and funding
5 authors.
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Abstract
Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.
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