title: Analysis of sequence-dependent curvature in matrix attachment regions.
abstract: Sequence-dependent DNA conformations of matrix attachment regions (MARs) available in a database were calculated using the wedge model, and compared with randomly chosen genes, promoters, enhancers and transposons. The MARs had a longer bent part and higher angle/helical turn than the other regions. It is known that some MAR sequences have A-tracts that cause DNA bending, and we also found many A-tracts in examined MARs. Furthermore, non-random and clustered distribution of A-tracts shown here gave further evidence of the importance of A-tracts for MAR conformations. These results suggest that DNAs of MARs have a characteristic conformation instead of conserved sequence.
authors.affiliation: Institute of Agriculture and Forestry, University of Tsukuba, Ibaraki 305-8572, Tsukuba, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Yamamura
authors.forename: K
authors.initials: K
authors.lastname: Nomura
mesh_terms: D000818:Animals; D001483:Base Sequence; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D012984:Software
chemical_list: D004247:DNA