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Nucleic Acids Research, Vol 26, Issue 21 4811-4817, Copyright © 1998 by Oxford University Press

ARTICLES

Suppression of electrophoretic anomaly of bent DNA segments by the structural property that causes rapid migration

T Ohyama, H Tsujibayashi, H Tagashira, K Inano, T Ueda, Y Hirota and K Hashimoto
Department of Biology, Faculty of Science, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658, Japan. Niigata 951, Japan, ohyama@base2.ipc.konan-u.ac.jp

Intrinsic DNA curvature is speculated to be a common feature of all satellite DNA sequences and may aid in the tight winding of DNA in constitutive heterochromatin. Several satellite DNAs, however, show unusually rapid migration in non-denaturing polyacrylamide gels, which is just the opposite behavior of that shown by curved DNA structures. Employing bovine satellite I DNA monomer, we attempted to understand the molecular mechanism of 'rapid migration'. The phenomenon of rapid migration was temperature-dependent and to a small extent polyacrylamide-concentration-dependent. Physiological or near- physiological concentrations of Mg2+and Ca2+ions bent the rapid migrating DNA segment. Predominance of purine-purine base stacking over purine-pyrimidine in nucleotide sequence was strongly indicated to be the cause of the rapid migration. Furthermore, they seemed to be implicated in the formation of induced DNA bend. We also found that the satellite I monomer contains an intrinsic DNA curvature as do many other satellites. Heretofore, the rapid migration property has concealed the presence of curvature.
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