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PMID: 2827112 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Helical phasing between DNA bends and the determination of bend direction.

Nucleic acids research ·Vol. 15 ·No. 23 ·1987-12-10 ·Pages 9771-9

Salvo JJ, Grindley ND

Abstract

The presence and location of bends in DNA can be inferred from the anomalous mobility of DNA fragments or protein-DNA complexes during electrophoresis in polyacrylamide gels. Direction of bending is not so easily determined. We show here that a protein-induced bend, when linked to a protein-independent DNA bend by a segment of variable length, exhibits an electrophoretic mobility that varies in a sinusoidal manner with the length of the linker. Mobility minima occur once for each addition to the linker of one helical turn of DNA. Since minima should occur when two bends reinforce one another, the direction of one bend relative to the other can be determined from the distances between the two centers of bending at which minima occur. Our results strongly support the idea that the A5-6 tracts in kinetoplast DNA bend towards the minor groove while the bend at the recombination site of the gamma delta resolvase (binding site I of the gamma delta res site) bends towards the major groove.

MeSH Terms
Animals Base Sequence Electrophoresis, Polyacrylamide Gel Leishmania/genetics Models, Genetic Nucleic Acid Conformation Nucleotidyltransferases Plasmids Transposases
Chemicals
Nucleotidyltransferases Transposases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Salvo J J
Yale University School of Medicine, Department of Molecular Biophysics and Biochemistry, New Haven, CT 06510.
Grindley N D
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Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/15.23.9771
Published
1987-12-10
Pages
9771-9
Language
English
Region
England
NLM ID
0411011
PMCID
PMC306530
Subset
IM
Grants
NIGMS NIH HHS · GM28470 · United States
External Links
PubMed source DOI: 10.1093/nar/15.23.9771 PMC Full Text View journal details
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