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

E. B. Starikov ; D. Hennig ; H. Yamada ; R. Gutierrez ; Bengt Nordén (Institutionen för kemi- och bioteknik, Fysikalisk kemi) ; G. Cuniberti
Biophysical Reviews and Letters (17930480). Vol. 4 (2009), 3, p. 209-230.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: DNA; Nanopore translocation; Screw; Screw and nut; Screw-jack



Denna post skapades 2017-12-27.
CPL Pubid: 254099

 

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Institutioner (Chalmers)

Institutionen för kemi- och bioteknik, Fysikalisk kemi (2005-2014)

Ämnesområden

Fysikalisk kemi

Chalmers infrastruktur