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Biochemistry. 2005 Oct 11;44(40):13225-34.

RNA challenges for computational chemists.

Author information

1
Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA.

Abstract

Some experimental results for the thermodynamics of RNA folding cannot be explained by simple pairwise hydrogen-bonding models. Such effects include the stabilities of isoguanosine-isocytidine (iG-iC) base pairs and of various 2 x 2 nucleotide internal loops. Presumably, these results can be explained by base stacking effects, which can be partitioned into Coulombic and overlap effects. We review experimental measurements that provide benchmarks for testing the approximations and theories used for modeling nucleic acids. Quantitative agreement between experiment and theory will indicate understanding of the interactions determining RNA stability and structure.

PMID:
16201748
PMCID:
PMC3738067
DOI:
10.1021/bi051236o
[Indexed for MEDLINE]
Free PMC Article

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