Improved quantitation of DNA curvature using ligation ladders

Eric D. Ross, Robert B. Den, Philip R. Hardwidge, L James Maher III

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

It is often desirable to estimate accurately the local shape of DNA molecules. Such measurements are useful in understanding the intrinsic contribution of DNA sequence to curvature, as well as in assessing the effects of chemical modifications. We have been investigating the effects of asymmetric phosphate neutralization on DNA shape using the well-characterized ligation ladder approach developed by Crothers and co-workers. This technique is remarkably sensitive to differences in DNA shape. We now report a general quantitative assay of DNA curvature that we have validated using a set of phased A5 tract standards. This approach allows simultaneous estimation of helix axis deflection magnitude and direction when a test sequence is monitored in at least three phasings relative to a reference A5-6 tract in short DNA duplexes. Analysis using this improved approach confirms our published data on DNA curvature due to electrostatic effects.

Original languageEnglish (US)
Pages (from-to)4135-4142
Number of pages8
JournalNucleic Acids Research
Volume27
Issue number21
DOIs
StatePublished - Nov 1 1999

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Ligation
DNA
Static Electricity
Phosphates

ASJC Scopus subject areas

  • Genetics

Cite this

Improved quantitation of DNA curvature using ligation ladders. / Ross, Eric D.; Den, Robert B.; Hardwidge, Philip R.; Maher III, L James.

In: Nucleic Acids Research, Vol. 27, No. 21, 01.11.1999, p. 4135-4142.

Research output: Contribution to journalArticle

Ross, Eric D. ; Den, Robert B. ; Hardwidge, Philip R. ; Maher III, L James. / Improved quantitation of DNA curvature using ligation ladders. In: Nucleic Acids Research. 1999 ; Vol. 27, No. 21. pp. 4135-4142.
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