Screw Motion of Dna Duplex During Translocation Through Pore I: Introduction of the Coarse-Grained Model

Abstract

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.

Active polymer translocation in the three-dimensional domain

“…The passage of polymers thorough the nanopores is also important in many chemical and industrial processes. In this context, nanotechnological applications try to emulate the complex biological processes involved in the translocation problem [4][5][6].…”

Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor

“…[1] The passage of polymers thorough nanopores is also a fundamental problem in chemical and industrial processes. In this context, many efforts are made in nanotechnological applications, that try to emulate the complex biological processes involved in the translocation problem [2][3][4]. An important related application is the use of nanopores to unzip and translocate single DNA chains with the purpose of perform fast and detailed DNA sequencing [5][6][7][8][9].…”

Modeling the mechanochemistry of theϕ29DNA translocation motor

“…Recently a model has been presented in order to describe the main features of the φ29 bacteriophage translocation dynamics [12], as a biological extension of a time varying driven translocation of long molecules [13,14]. The idea of the model is to drive a polymer chain in one direction with a constant force, while in its activated state, but leave the polymer to diffuse freely when the motor is inactive [12,15,16]. The mechanism is the origin of the Michaelis-Menten (MM) polymer velocity, related to a microscopic reinterpretation of the MM enzymatic reaction [12].…”