Literature DB >> 17025468

How does a protein search for the specific site on DNA: The role of disorder.

Tao Hu1, B I Shklovskii.   

Abstract

Proteins can locate their specific targets on DNA up to two orders of magnitude faster than the Smoluchowski three-dimensional diffusion rate. This happens due to nonspecific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such a one-dimensional route towards the target an "antenna." We studied the role of the dispersion of nonspecific binding energies within the antenna due to a quasirandom sequence of natural DNA. A random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for macroscopic and mesoscopic antennas.

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Year:  2006        PMID： 17025468     DOI： 10.1103/PhysRevE.74.021903

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN： 1539-3755


  11 in total

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2.  Dynamic strategies for target-site search by DNA-binding proteins.

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4.  Are DNA transcription factor proteins maxwellian demons?

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Journal:  Biophys J       Date:  2008-05-02       Impact factor: 4.033

5.  The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI.

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Journal:  Biophys J       Date:  2019-05-08       Impact factor: 4.033

6.  DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping.

Authors:  Nina Y Sidorova; Thomas Scott; Donald C Rau
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Review 7.  Dancing on DNA: kinetic aspects of search processes on DNA.

Authors:  Anahita Tafvizi; Leonid A Mirny; Antoine M van Oijen
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Review 8.  Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins.

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Journal:  Prog Biophys Mol Biol       Date:  2016-12-08       Impact factor: 3.667

Review 9.  Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.

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Journal:  Chem Rev       Date:  2009-09       Impact factor: 60.622

10.  Spatial effects on the speed and reliability of protein-DNA search.

Authors:  Zeba Wunderlich; Leonid A Mirny
Journal:  Nucleic Acids Res       Date:  2008-05-03       Impact factor: 16.971
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