Dynamics of site juxtaposition in supercoiled DNA

Jing Huang, Tamar Schlick, Alexander Vologodskii

Research output: Contribution to journalArticlepeer-review

Abstract

Juxtaposition kinetics between specific sites in supercoiled DNA is investigated at close to physiological ionic conditions by Brownian dynamics simulations. At such conditions, supercoiled DNA is interwound, and the probability of spatial site juxtaposition is much higher than in relaxed DNA. We find, however, that supercoiling does not correspondingly increase the rate of juxtaposition at these physiological conditions. An explanation to this unexpected finding emerges on analysis of the juxtaposition dynamics. We note that although a particular site i1 in supercoiled DNA is often in close proximity (juxtaposed) to another site i2, the change of i2 occurs very slowly and depends largely on internal slithering of opposite segments of the DNA superhelix. Such slithering results in long correlations between successive values of i2; these correlations increase the average time of juxtaposition between two DNA sites. Random collisions between sites located on different superhelix branches - although increasing in importance with DNA size - contribute less substantially to site juxtaposition at high salt than slithering for DNA up to 6 kb in length.

Original languageEnglish (US)
Pages (from-to)968-973
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume98
Issue number3
DOIs
StatePublished - Jan 30 2001

ASJC Scopus subject areas

  • General

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