T. Ohyama et al., SUPPRESSION OF ELECTROPHORETIC ANOMALY OF BENT DNA SEGMENTS BY THE STRUCTURAL PROPERTY THAT CAUSES RAPID MIGRATION, Nucleic acids research, 26(21), 1998, pp. 4811-4817
Intrinsic DNA curvature is speculated to be a common feature of all sa
tellite DNA sequences and may aid in the tight winding of DNA in const
itutive heterochromatin. Several satellite DNAs, however, show unusual
ly rapid migration in non-denaturing polyacrylamide gels, which is jus
t the opposite behavior of that shown by curved DNA structures. Employ
ing bovine satellite I DNA monomer, we attempted to understand the mol
ecular mechanism of 'rapid migration'. The phenomenon of rapid migrati
on was temperature-dependent and to a small extent polyacrylamide-conc
entration-dependent. Physiological or near-physiological concentration
s of Mg2+ and Ca2+ ions bent the rapid migrating DNA segment, Predomin
ance of purine-purine base stacking over purine-pyrimidine in nucleoti
de sequence was strongly indicated to be the cause of the rapid migrat
ion, Furthermore, they seemed to be implicated in the formation of ind
uced DNA bend. We also found that the satellite I monomer contains an
intrinsic DNA curvature as do many other satellites, Heretofore, the r
apid migration property has concealed the presence of curvature.