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Nucleic Acids Research, Vol 26, Issue 8 1899-1905, Copyright © 1998 by Oxford University Press

ARTICLES

DNA fragments with specific nucleotide sequences in their single- stranded termini exhibit unusual electrophoretic mobilities

I Muiznieks and W Doerfler
Institute for Genetics, University of Cologne, Weyertal 121, D-50931 Cologne, Germany.

DNA restriction fragments, 120-650 base pairs (bp) in length, with 5'- GCGC-3', 5'-GGCC-3' or 3'-GCGC-5' single-stranded overhanging termini, give rise to diffuse bands of unusual electrophoretic mobility in non- denaturing polyacrylamide gels. This shift in electrophoretic mobility can be observed at 4-12 degreesC, not at higher temperatures, but is stabilized by 5-10 mM Mg2+, even at 37 degreesC. The nucleotide sequence in the abutting double-stranded part of the fragment does not affect this phenomenon, which is not caused by dimerization. The altered mobility may be due to the unusual terminal DNA structure, which is dependent on co-operative interactions among more than two neighboring G and C residues. The structure is stabilized by cytidine methylation. The biological role of such fragment structures in DNA repair and recombination is presently unknown.
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Q. Liu, W. A. Scaringe, and S. S. Sommer
Discrete mobility of single-stranded DNA in non-denaturing gel electrophoresis
Nucleic Acids Res., February 15, 2000; 28(4): 940 - 943.
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