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Distribution of bending propensity in DNA sequences
Author(s) -
Gabrielian Andrei,
Simoncsits András,
Pongor Sándor
Publication year - 1996
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/0014-5793(96)00837-x
Subject(s) - dna , genome , oligonucleotide , curvature , cleavage (geology) , biology , bending , nucleosome , restriction enzyme , computational biology , genetics , physics , geometry , histone , mathematics , gene , paleontology , fracture (geology) , thermodynamics
Local binding propensity and curvature of DNA can be characterized using a vector description of DNA bendability, based on a set of parameters derived from deoxyribonuclease I (DNase I) cleavage experiments. Two characteristics — arithmetic and vector averages of bendability — were successfully used to predict experimentally known bendable, rigid and curved segments in DNA. A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenza genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments — similar to artificially designed curved oligonucleotides — are extremely rare in natural DNA.