Determination of the Extent of DNA Bending by an Adenine-Thymine Tract

Hyeon-Sook Koo, Jacqueline Drak, Janet A. Rice, Donald M. Crothers

Research output: Contribution to journalArticle

200 Citations (Scopus)

Abstract

We determined the magnitude of the bend induced in DNA by an adenine-thymine tract by measuring the rate of cyclization of DNA oligonucleotides containing phased A tracts. A series of linear multimers with 2-bp single-stranded ends, in which the (A•T)6 tracts are separated by CG2-3C sequences and are positioned 10 and 11 bp apart alternately, were prepared from 21 bp long synthetic duplexed deoxyoligonucleotides. The cyclization rates of the multimers (105–210 bp) and the bimolecular association rate of the 84 bp long multimer were measured in the presence of DNA ligase. From the rate constants of the cyclization and bimolecular association reactions, ring closure probabilities were obtained for the multimers. The systematically bent molecules were simulated by Monte Carlo methods, and the ring closure probabilities were calculated for a given set of junction bend angles. By comparing the calculated values of ring closure probabilities to experimental values and adjusting the junction bend angles to fit experimental values, the extent of bending at the junctions (or the extent of bending for an adenine tract) was determined. We conclude that an A6 tract bends the DNA helix by 17–21°.

Original languageEnglish
Pages (from-to)4227-4234
Number of pages8
JournalBiochemistry
Volume29
Issue number17
DOIs
Publication statusPublished - 1990 Mar 1

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Thymine
Cyclization
Adenine
DNA
Association reactions
DNA Ligases
Monte Carlo Method
Oligonucleotides
Rate constants
Monte Carlo methods
Molecules

All Science Journal Classification (ASJC) codes

  • Biochemistry

Cite this

Koo, Hyeon-Sook ; Drak, Jacqueline ; Rice, Janet A. ; Crothers, Donald M. / Determination of the Extent of DNA Bending by an Adenine-Thymine Tract. In: Biochemistry. 1990 ; Vol. 29, No. 17. pp. 4227-4234.
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Determination of the Extent of DNA Bending by an Adenine-Thymine Tract. / Koo, Hyeon-Sook; Drak, Jacqueline; Rice, Janet A.; Crothers, Donald M.

In: Biochemistry, Vol. 29, No. 17, 01.03.1990, p. 4227-4234.

Research output: Contribution to journalArticle

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