Gapped DNA and cyclization of short DNA fragments

Quan Du, Maria Vologodskaia, Heiko Kuhn, Maxim Frank-Kamenetskii, Alexander Vologodskii

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

We use the cyclization of small DNA molecules, ∼200 bp in length, to study conformational properties of DNA fragments with single-stranded gaps. The approach is extremely sensitive to DNA conformational properties and, being complemented by computations, allows a very accurate determination of the fragment's conformational parameters. Sequence-specific nicking endonucleases are used to create the 4-nt-long gap. We determined the bending rigidity of the single-stranded region in the gapped DNA. We found that the gap of 4 nt in length makes all torsional orientations of DNA ends equally probable. Our results also show that the gap has isotropic bending rigidity. This makes it very attractive to use gapped DNA in the cyclization experiments to determine DNA conformational properties, since the gap eliminates oscillations of the cyclization efficiency with the DNA length. As a result, the number of measurements is greatly reduced in the approach, and the analysis of the data is greatly simplified. We have verified our approach on DNA fragments containing well-characterized intrinsic bends caused by A-tracts. The obtained experimental results and theoretical analysis demonstrate that gapped-DNA cyclization is an exceedingly sensitive and accurate approach for the determination of DNA bending.

Original languageEnglish (US)
Pages (from-to)4137-4145
Number of pages9
JournalBiophysical Journal
Volume88
Issue number6
DOIs
StatePublished - Jun 2005
Externally publishedYes

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Cyclization
DNA
Endonucleases

ASJC Scopus subject areas

  • Biophysics

Cite this

Du, Q., Vologodskaia, M., Kuhn, H., Frank-Kamenetskii, M., & Vologodskii, A. (2005). Gapped DNA and cyclization of short DNA fragments. Biophysical Journal, 88(6), 4137-4145. https://doi.org/10.1529/biophysj.104.055657

Gapped DNA and cyclization of short DNA fragments. / Du, Quan; Vologodskaia, Maria; Kuhn, Heiko; Frank-Kamenetskii, Maxim; Vologodskii, Alexander.

In: Biophysical Journal, Vol. 88, No. 6, 06.2005, p. 4137-4145.

Research output: Contribution to journalArticle

Du, Q, Vologodskaia, M, Kuhn, H, Frank-Kamenetskii, M & Vologodskii, A 2005, 'Gapped DNA and cyclization of short DNA fragments', Biophysical Journal, vol. 88, no. 6, pp. 4137-4145. https://doi.org/10.1529/biophysj.104.055657
Du Q, Vologodskaia M, Kuhn H, Frank-Kamenetskii M, Vologodskii A. Gapped DNA and cyclization of short DNA fragments. Biophysical Journal. 2005 Jun;88(6):4137-4145. https://doi.org/10.1529/biophysj.104.055657
Du, Quan ; Vologodskaia, Maria ; Kuhn, Heiko ; Frank-Kamenetskii, Maxim ; Vologodskii, Alexander. / Gapped DNA and cyclization of short DNA fragments. In: Biophysical Journal. 2005 ; Vol. 88, No. 6. pp. 4137-4145.
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