title: 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.
authors.affiliation: Department of Tumor Biology, The Norwegian Radium Hospital, N-0310 Oslo, Norway.
authors.forename: Eivind
authors.initials: E
authors.lastname: Tøstesen
mesh_terms: D000465:Algorithms; D010582:Bacteriophage lambda / Q000235:genetics; D001483:Base Sequence; D003198:Computer Simulation; D004279:DNA, Viral / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D017422:Sequence Analysis, DNA / Q000379:methods*; D013329:Structure-Activity Relationship; D013696:Temperature; D044366:Transition Temperature
chemical_list: D004279:DNA, Viral