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.
- Publication:
-
Physical Review E
- Pub Date:
- June 2005
- DOI:
- 10.1103/PhysRevE.71.061922
- arXiv:
- arXiv:q-bio/0404019
- Bibcode:
- 2005PhRvE..71f1922T
- Keywords:
-
- 87.14.Gg;
- 87.15.Ya;
- 05.70.Fh;
- 02.70.Rr;
- DNA RNA;
- Fluctuations;
- Phase transitions: general studies;
- General statistical methods;
- Quantitative Biology - Biomolecules;
- Quantitative Biology - Genomics
- E-Print:
- 11 pages, 9 figures