The helical structure of DNA facilitates binding

The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast...

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Bibliographic Details
Published in:Journal of physics. A, Mathematical and theoretical Mathematical and theoretical, 2016-09, Vol.49 (36), p.364002
Main Authors: Berg, Otto G, Mahmutovic, Anel, Marklund, Emil, Elf, Johan
Format: Article
Language:English
Subjects:
diffusion limited
helix geometry
reaction-diffusion equation
steric constraints
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Summary:The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.
ISSN:1751-8113
1751-8121
1751-8121
DOI:10.1088/1751-8113/49/36/364002