How proteins search for their specific sites on DNA: The role of DNA conformation

Tao Hu, A. Yu Grosberg, B. I. Shklovskii

    Research output: Contribution to journalArticle

    Abstract

    It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.

    Original languageEnglish (US)
    Pages (from-to)2731-2744
    Number of pages14
    JournalBiophysical Journal
    Volume90
    Issue number8
    DOIs
    StatePublished - Apr 2006

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    Nucleic Acid Conformation
    DNA
    Proteins
    Deceleration
    Osmolar Concentration
    Molecular Biology

    ASJC Scopus subject areas

    • Biophysics

    Cite this

    How proteins search for their specific sites on DNA : The role of DNA conformation. / Hu, Tao; Grosberg, A. Yu; Shklovskii, B. I.

    In: Biophysical Journal, Vol. 90, No. 8, 04.2006, p. 2731-2744.

    Research output: Contribution to journalArticle

    Hu, Tao ; Grosberg, A. Yu ; Shklovskii, B. I. / How proteins search for their specific sites on DNA : The role of DNA conformation. In: Biophysical Journal. 2006 ; Vol. 90, No. 8. pp. 2731-2744.
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