Partly melted DNA conformations obtained with a probability peak finding method

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.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio