Screw motion of DNA duplex during translocation through pore. I. Introduction of the coarse-grained model
Artikel i vetenskaplig tidskrift, 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

DNA

Screw

Screw-jack

Författare

Evgeni B. Starikov

Karlsruhe Institute of Technology, Campus South

Technische Universitat Dresden

D. Hennig

Humboldt-Universitat zu Berlin

H. Yamada

Yamada Physics Research Laboratory

R. Gutierrez

Technische Universitat Dresden

Bengt Nordén

Chalmers, Kemi- och bioteknik, Fysikalisk kemi

G. Cuniberti

Technische Universitat Dresden

Biophysical Reviews and Letters

1793-0480 (ISSN)

Vol. 4 209-230

Ämneskategorier

Fysikalisk kemi

DOI

10.1142/S1793048009000995