Nucleic acid duplex stability: influence of base composition on cation effects

Nucleic Acids Res. 1999 Jul 15;27(14):2957-65. doi: 10.1093/nar/27.14.2957.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Composition*
  • Base Pairing / drug effects
  • Base Sequence
  • Binding, Competitive
  • Buffers
  • Cations / metabolism
  • Cations / pharmacology*
  • Cations, Divalent / metabolism
  • Cations, Divalent / pharmacology
  • Cations, Monovalent / metabolism
  • Cations, Monovalent / pharmacology
  • Circular Dichroism
  • Dose-Response Relationship, Drug
  • Nucleic Acid Heteroduplexes / chemistry
  • Nucleic Acid Heteroduplexes / genetics
  • Nucleic Acid Heteroduplexes / metabolism*
  • Nucleic Acid Hybridization / drug effects
  • Oligonucleotides / chemistry
  • Oligonucleotides / genetics
  • Oligonucleotides / metabolism
  • Sodium Chloride / metabolism
  • Sodium Chloride / pharmacology
  • Temperature
  • Thermodynamics


  • Buffers
  • Cations
  • Cations, Divalent
  • Cations, Monovalent
  • Nucleic Acid Heteroduplexes
  • Oligonucleotides
  • Sodium Chloride