Analysis of sequence-dependent curvature in matrix attachment regions

FEBS Lett. 2001 Feb 2;489(2-3):166-70. doi: 10.1016/s0014-5793(01)02098-1.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Computer Graphics
  • DNA / chemistry*
  • DNA / metabolism
  • Humans
  • Molecular Sequence Data
  • Nuclear Matrix / metabolism*
  • Nucleic Acid Conformation
  • Software

Substances

  • DNA