Supercoiling-induced DNA bending

Jeffrey W. Pavlicek, Elena A. Oussatcheva, Richard R. Sinden, Vladimir N. Potaman, Otto F. Sankey, Yuri L Lyubchenko

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Local DNA bending is a critical factor for numerous DNA functions including recognition of DNA by sequence-specific regulatory binding proteins. Negative DNA supercoiling increases both local and global DNA dynamics, and this dynamic flexibility can facilitate the formation of DNA-protein complexes. We have recently shown that apexes of supercoiled DNA molecules are sites that can promote the formation of an alternative DNA structure, a cruciform, suggesting that these positions in supercoiled DNA are under additional stress and perhaps have a distorted DNA geometry. To test this hypothesis, we used atomic force microscopy to directly measure the curvature of apical positions in supercoiled DNA. The measurements were performed for an inherently curved sequence formed by phased A tracts and a region of mixed sequence DNA. For this, we used plasmids in which an inverted repeat and A tract were placed at precise locations relative to each other. Under specific conditions, the inverted repeat formed a cruciform that was used as a marker for the unambiguous identification of the A tract location. When the A tract and cruciform were placed diametrically opposite, this yielded predominantly nonbranched plectonemic molecules with an extruded cruciform and A tract localized in the terminal loops. For both the curved A tract and mixed sequence nonbent DNA, their localization to an apex increased the angle of bending compared to that expected for DNA unconstrained in solution. This is consistent with increased helical distortion at an apical bend.

Original languageEnglish (US)
Pages (from-to)10664-10668
Number of pages5
JournalBiochemistry
Volume43
Issue number33
DOIs
StatePublished - Aug 24 2004

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DNA
Superhelical DNA
DNA sequences
Atomic Force Microscopy
Molecules
Carrier Proteins
Plasmids
Atomic force microscopy
Geometry
Proteins

ASJC Scopus subject areas

  • Biochemistry

Cite this

Pavlicek, J. W., Oussatcheva, E. A., Sinden, R. R., Potaman, V. N., Sankey, O. F., & Lyubchenko, Y. L. (2004). Supercoiling-induced DNA bending. Biochemistry, 43(33), 10664-10668. https://doi.org/10.1021/bi0362572

Supercoiling-induced DNA bending. / Pavlicek, Jeffrey W.; Oussatcheva, Elena A.; Sinden, Richard R.; Potaman, Vladimir N.; Sankey, Otto F.; Lyubchenko, Yuri L.

In: Biochemistry, Vol. 43, No. 33, 24.08.2004, p. 10664-10668.

Research output: Contribution to journalArticle

Pavlicek, JW, Oussatcheva, EA, Sinden, RR, Potaman, VN, Sankey, OF & Lyubchenko, YL 2004, 'Supercoiling-induced DNA bending', Biochemistry, vol. 43, no. 33, pp. 10664-10668. https://doi.org/10.1021/bi0362572
Pavlicek JW, Oussatcheva EA, Sinden RR, Potaman VN, Sankey OF, Lyubchenko YL. Supercoiling-induced DNA bending. Biochemistry. 2004 Aug 24;43(33):10664-10668. https://doi.org/10.1021/bi0362572
Pavlicek, Jeffrey W. ; Oussatcheva, Elena A. ; Sinden, Richard R. ; Potaman, Vladimir N. ; Sankey, Otto F. ; Lyubchenko, Yuri L. / Supercoiling-induced DNA bending. In: Biochemistry. 2004 ; Vol. 43, No. 33. pp. 10664-10668.
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