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Screw motion of DNA...
Screw motion of DNA duplex during translocation through pore. I. Introduction of the coarse-grained model
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- Starikov, Evgeni B. (author)
- Karlsruher Institut für Technologie (KIT),Karlsruhe Institute of Technology (KIT),Technische Universität Dresden
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- Hennig, D. (author)
- Humboldt-Universität zu Berlin,Humboldt University of Berlin
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Yamada, H. (author)
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- Gutierrez, R. (author)
- Technische Universität Dresden
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- Nordén, Bengt, 1945 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Cuniberti, G. (author)
- Technische Universität Dresden
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(creator_code:org_t)
- 2009
- 2009
- English.
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In: Biophysical Reviews and Letters. - 1793-0480. ; 4:3, s. 209-230
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Abstract
Subject headings
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- 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.
Subject headings
- NATURVETENSKAP -- Kemi -- Fysikalisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Physical Chemistry (hsv//eng)
Keyword
- DNA
- Screw-jack
- Screw and nut
- Screw
- Nanopore translocation
Publication and Content Type
- art (subject category)
- ref (subject category)
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