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

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

2006-02-20

arxiv.org/abs/cond-mat/0602444v2

Phys. Rev. E 74, 021903 (2006)

Physics

Condensed Matter

Soft Condensed Matter

4 pages, 4 figures

Scientific paper

10.1103/PhysRevE.74.021903

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 non-specific adsorption of proteins to DNA and subsequent one-dimensional sliding along DNA. We call such one-dimensional route towards the target "antenna". We studied the role of the dispersion of nonspecific binding energies within the antenna due to quasi random sequence of natural DNA. Random energy profile for sliding proteins slows the searching rate for the target. We show that this slowdown is different for the macroscopic and mesoscopic antennas.

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