Calibration of DNA curvature and a unified description of sequence-directed bending

H. S. Koo, D. M. Crothers

Research output: Contribution to journalArticle

257 Citations (Scopus)

Abstract

Chemically synthesized duplex oligodeoxynucleotides having different average numbers of adenine tracts (A6) per helix turn were ligated into multimers and analyzed by electrophoresis on polyacrylamide gels. The magnitude of the anomaly in gel mobility is found to be a quadratic function of the curvature of the DNA molecule. Parameters that describe intrinsic DNA bending, expressed as the tilt and roll components of the helix-axis deflection at the junctions between the adenine tract and adjacent B-DNA, were adjusted to fit the measured relative curvature of regularly repeated DNA bending sequences known from other studies and synthesized for this study. The model developed here retains the predominance of bending in the direction of tilt at the junctions but incorporates an appreciable roll component at the 5' end of an adenine tract, opening the minor groove there. This feature is consistent with chemical 'footprinting' experiments on molecules containing adenine tracts. The overall direction of bending is effectively toward the minor groove, viewed from the center of an A5 or A6 tract. A possible underlying structure, which can also be described by a wedge bending model, is that derived from fiber diffraction studies of poly(dA) · poly(dT). However, alternative models for the adenine tract, such as propeller twisted DNA, cannot be eliminated, although they do not lead to the correct direction of bending. The results permit calculation of the helix-axis trajectory of natural DNA molecules containing adenine-tract bends.

Original languageEnglish
Pages (from-to)1763-1767
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume85
Issue number6
DOIs
Publication statusPublished - 1988 Dec 1

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Adenine
Calibration
DNA
Oligodeoxyribonucleotides
Polyacrylamide Gel Electrophoresis
Gels
Direction compound

All Science Journal Classification (ASJC) codes

  • General

Cite this

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abstract = "Chemically synthesized duplex oligodeoxynucleotides having different average numbers of adenine tracts (A6) per helix turn were ligated into multimers and analyzed by electrophoresis on polyacrylamide gels. The magnitude of the anomaly in gel mobility is found to be a quadratic function of the curvature of the DNA molecule. Parameters that describe intrinsic DNA bending, expressed as the tilt and roll components of the helix-axis deflection at the junctions between the adenine tract and adjacent B-DNA, were adjusted to fit the measured relative curvature of regularly repeated DNA bending sequences known from other studies and synthesized for this study. The model developed here retains the predominance of bending in the direction of tilt at the junctions but incorporates an appreciable roll component at the 5' end of an adenine tract, opening the minor groove there. This feature is consistent with chemical 'footprinting' experiments on molecules containing adenine tracts. The overall direction of bending is effectively toward the minor groove, viewed from the center of an A5 or A6 tract. A possible underlying structure, which can also be described by a wedge bending model, is that derived from fiber diffraction studies of poly(dA) · poly(dT). However, alternative models for the adenine tract, such as propeller twisted DNA, cannot be eliminated, although they do not lead to the correct direction of bending. The results permit calculation of the helix-axis trajectory of natural DNA molecules containing adenine-tract bends.",
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Calibration of DNA curvature and a unified description of sequence-directed bending. / Koo, H. S.; Crothers, D. M.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 6, 01.12.1988, p. 1763-1767.

Research output: Contribution to journalArticle

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