Free energy considerations for nucleic acids with dangling ends near a surface: Acoarse grained approach

J. Ambia-Garrido, Arnold Vainrub, B. Montgomery Pettitt

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

A coarse grained model for the thermodynamics of nucleic acid hybridization near surfaces has been extended and parameterized to consider the contribution of unpaired dangling ends. The parameters of the model differ when representing a double stranded DNA section or a single stranded DNA section. The thermodynamic effects of the possibility of different dangling end combinations were considered in the presence of different types of surfaces. Configurational sampling was achieved by the Metropolis Monte Carlo method. To gain a more complete picture of the free energy changes, an estimation of the conformational entropy was included. We find a strong thermodynamic effect for dangling mismatches due to sequence requirements when they are nearer the surface as opposed to being held away from the surface.

Original languageEnglish (US)
Article number325101
JournalJournal of Physics Condensed Matter
Volume23
Issue number32
DOIs
StatePublished - Aug 17 2011
Externally publishedYes

ASJC Scopus subject areas

  • Materials Science(all)
  • Condensed Matter Physics

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