Screw motion of DNA duplex during translocation through pore. I. Introduction of the coarse-grained model
Journal article, 2009

Based upon the structural properties of DNA duplexes and their counterion-water surrounding in solution, we have introduced here a screw model which may describe translocation of DNA duplexes through artificial nanopores of the proper diameter (where the DNA counterion-hydration shell can be intact) in a qualitatively correct way. This model represents DNA as a kind of "screw," whereas the counterion-hydration shell is a kind of "nut." Mathematical conditions for stable dynamics of the DNA screw model are investigated in detail. When an electrical potential is applied across an artificial membrane with a nanopore, the "screw" and "nut" begin to move with respect to each other, so that their mutual rotation is coupled with their mutual translation. As a result, there are peaks of electrical current connected with the mutual translocation of DNA and its counterion-hydration shell, if DNA is possessed of some non-regular base-pair sequence. The calculated peaks of current strongly resemble those observed in the pertinent experiments. An analogous model could in principle be applied to DNA translocation in natural DNA-protein complexes of biological interest, where the role of "nut" would be played by protein-tailored "channels." In such cases, the DNA screw model is capable of qualitatively explaining chemical-to-mechanical energy conversion in DNA-protein molecular machines via symmetry breaking in DNA-protein friction.



Screw and nut


Nanopore translocation


Evgeni B. Starikov

Karlsruhe Institute of Technology (KIT)

Technische Universität Dresden

D. Hennig

Humboldt University of Berlin

H. Yamada

Yamada Physics Research Laboratory

R. Gutierrez

Technische Universität Dresden

Bengt Nordén

Chalmers, Chemical and Biological Engineering, Physical Chemistry

G. Cuniberti

Technische Universität Dresden

Biophysical Reviews and Letters

1793-0480 (ISSN)

Vol. 4 3 209-230

Subject Categories

Physical Chemistry



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