Nucleic Acids Research, Vol 27, Issue 14 2957-2965, Copyright © 1999 by Oxford University Press
S Nakano, M Fujimoto, H Hara and N Sugimoto
The effects of counter ion on a nucleic acid duplex stability were
investigated. Since a linear free energy relationship for the
thermostability of oligonucleotide duplexes between those in 1 M and in 100
mM NaCl-phosphate buffer were observed regardless of whether they are
DNA-DNA, RNA-RNA or RNA-DNA duplexes, simple prediction systems for [Delta]
G degrees 37as well as T mvalues in 100 mM NaCl-phosphate buffer were
established. These predictions were successful with an average error of
only 2.4 degrees C for T mand 5. 7% for G degrees 37values. The number of
Na+newly bound to a duplex when the duplex forms (-[Delta] n) was
significantly influenced by the base composition, and -[Delta] n for
d(GCCAGTTAA)/d(TTAACTGGC) was different for MgCl2, CaCl2, BaCl2and
MnCl2(from 0.70 to 0.76 with the same order of the duplex stability).
Almost no additive effects on the duplex stability was observed for NaCl
and MgCl2, suggesting a competitive binding for these cations. The
sequence-dependent manner of [Delta] n suggests the presence of
preferential base pairs or nearest-neighbor base pairs for the cation
binding, which would affect nearest-neighbor parameters.
ARTICLES
Nucleic acid duplex stability: influence of base composition on cation effects
Department of Chemistry, Faculty of Science, High Technology Research Center, Konan University,8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
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