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Nucleic Acids Research, Vol 24, Issue 22 4501-4505, Copyright © 1996 by Oxford University Press

ARTICLES

Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes

N Sugimoto, S Nakano, M Yoneyama and K Honda
Department of Chemistry, Faculty of Science, Konan University, Kobe, Japan. sugimoto@konan-u.ac.jp

To improve the previous DNA/DNA nearest-neighbor parameters, thermodynamic parameters (deltaH degrees, deltaS degrees and deltaG degrees) of 50 DNA/DNA duplexes were measured. Enthalpy change of a helix initiation factor is also considered though the parameters reported recently did not contain the factor. A helix initiation factor for DNA/DNA duplex determined here was the same as that of RNA/RNA duplex (deltaG degrees(37) = 3.4 kcal/mol). The improved nearest- neighbor parameters reproduced not only these 50 experimental values used here but also 15 other experimental values obtained in different studies. Comparing deltaG degrees(37) values of DNA/DNA nearest- neighbor parameters obtained here with those of RNA/RNA and RNA/DNA, RNA/RNA duplex was generally the most stable of the three kinds of duplexes with the same nearest-neighbor sequences. Which is more stable between DNA/DNA and RNA/DNA duplexes is sequence dependent.
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