Partly melted DNA conformations obtained with a probability peak finding method

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Jun;71(6 Pt 1):061922. doi: 10.1103/PhysRevE.71.061922. Epub 2005 Jun 28.

Abstract

Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. This yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. This article describes the methodology and discusses stitch profiles vs the ordinary probability profiles using the phage lambda genome as an example.

Publication types

  • Evaluation Study

MeSH terms

  • Algorithms
  • Bacteriophage lambda / genetics
  • Base Sequence
  • Computer Simulation
  • DNA, Viral / analysis
  • DNA, Viral / chemistry*
  • DNA, Viral / ultrastructure*
  • Models, Chemical*
  • Models, Molecular*
  • Models, Statistical
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Sequence Analysis, DNA / methods*
  • Structure-Activity Relationship
  • Temperature
  • Transition Temperature

Substances

  • DNA, Viral