Evaluation of some S/MAR sequence properties on DNA sequences involved in tightly bound DNA protein complexes of murine cells

Abstract

Abbreviations: MEL – Friend erythroleukemia cells; TBD – eukaryotic non-histone proteins tightly bound to DNA; S/MARs – conserved DNA sequences associated with matrix and/or scaffold Here we report the DNA sequence-based characterization of DNA fragments involved in stable complexes with proteins in mouse chromatin. Computer analysis of nine independently isolated and sequenced clones containing such sequences revealed some similar properties known to comprise S/MAR sequences. These characteristics (ori signals, TA, CA, TG richness, curved DNA, topoisomerase II binding sites) suggest that DNAs presented in tightly DNA-bound complexes have a certain characteristic sequence and conformation properties typical of S/MARs. Keywords: chromosomal DNA loops, nuclear matrix DNA, S/MAR sequences