Effect of inert tails on the thermodynamics of DNA hybridization

J Am Chem Soc. 2014 May 7;136(18):6538-41. doi: 10.1021/ja500027v. Epub 2014 Apr 23.

Abstract

The selective hybridization of DNA is of key importance for many practical applications such as gene detection and DNA-mediated self-assembly. These applications require a quantitative prediction of the hybridization free energy. Existing methods ignore the effects of non-complementary ssDNA tails beyond the first unpaired base. We use experiments and simulations to show that the binding strength of complementary ssDNA oligomers is altered by these sequences of non-complementary nucleotides. Even a small number of non-binding bases are enough to raise the hybridization free energy by approximately 1 kcal/mol at physiological salt concentrations. We propose a simple analytical expression that accounts quantitatively for this variation as a function of tail length and salt concentration.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemistry*
  • Nucleic Acid Hybridization*
  • Thermodynamics*

Substances

  • DNA