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Thermodynamic contributions of single internal rAdA, rCdC, rGdG and rUdT mismatches in RNA/DNA duplexes

Nucleic Acids Research, ISSN: 0305-1048, Vol: 39, Issue: 5, Page: 1894-1902
2011
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Article Description

The thermodynamic contributions of rAdA, rCdC, rGdG and rUdT single internal mismatches were measured for 54 RNA/DNA duplexes in a 1M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using the curve-fitting program Meltwin. The weighted average thermodynamic data were fit using singular value decomposition to determine the eight non-unique nearest-neighbor parameters for each internal mismatch. The new parameters predict the ΔG°37, ΔH° and melting temperature (Tm) of duplexes containing these single mismatches within an average of 0.33kcal/mol, 4.5kcal/mol and 1.4°C, respectively. The general trend in decreasing stability for the single internal mismatches is rGdG>rUdT>rAdA>rCdC. The stability trend for the base pairs 5′ of the single internal mismatch is rGdC>rCdG>rAdT>rUdA. The stability trend for the base pairs 3′ of the single internal mismatch is rCdG>rGdC >> rAdT>rUdA. These nearest-neighbor values are now a part of a complete set of single internal mismatch thermodynamic parameters for RNA/DNA duplexes that are incorporated into the nucleic acid assay development software programs Visual oligonucleotide modeling platform (OMP) and ThermoBLAST. © 2010 The Author(s).

Bibliographic Details

Norman E. Watkins Jr; William J. Kennelly; Mike J. Tsay; Astrid Tuin; Lara Swenson; Hyung-Ran Lee; Svetlana Morosyuk; Donald A. Hicks; John SantaLucia Jr

Oxford University Press (OUP)

Biochemistry, Genetics and Molecular Biology

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