Translocation of polymers with folded configurations across nanopores

Kotsev, Stanislav; Kolomeisky, Anatoly B.

doi:10.1063/1.2800008

Cited by 17 publications

(12 citation statements)

References 45 publications

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“…In this technique, individual molecules are mechanically or electrically forced through the nanopore, causing a temporary blockade of an ionic current passing through the pore. The duration of this blockade can report on the molecules' length or degree of folding,2 while its magnitude reports on the molecules' local size and charge distribution inside the nanopore 3–6. Using this approach, it is possible to detect the presence of double‐stranded7 and single‐stranded nucleic acids,8, 9 and to distinguish single‐stranded from double‐stranded nucleic acids within the same sample 10.…”

Section: Introductionmentioning

confidence: 99%

The Passage of Homopolymeric RNA through Small Solid‐State Nanopores

Hout

Skinner

Klijnhout

et al. 2011

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Solid-state nanopores are widely acknowledged as tools with which to study local structure in biological molecules. Individual molecules are forced through a nanopore, causing a characteristic change in an ionic current that depends on the molecules' local diameter and charge distribution. Here, the translocation measurements of long (~5-30 kilobases) single-stranded poly(U) and poly(A) molecules through nanopores ranging from 1.5 to 8 nm in diameter are presented. Individual molecules are found to be able to cause multiple levels of conductance blockade upon traversing the pore. By analyzing these conductance blockades and their relative incidence as a function of nanopore diameter, it is concluded that the smallest conductance blockades likely correspond to molecules that translocate through the pore in predominantly head-to-tail fashion. The larger conductance blockades are likely caused by molecules that arrive at the nanopore entrance with many strands simultaneously. These measurements constitute the first demonstration that single-stranded RNA can be captured in solid-state nanopores that are smaller than the diameter of double-stranded RNA. These results further the understanding of the conductance blockades caused by nucleic acids in solid-state nanopores, relevant for future applications, such as the direct determination of RNA secondary structure.

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Section: Introductionmentioning

confidence: 99%

The Passage of Homopolymeric RNA through Small Solid‐State Nanopores

Hout

Skinner

Klijnhout

et al. 2011

Small

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“…This is especially true, if we consider the presence of multiple binding sites within the nanopore interior that pull the polypeptides into the pore. This electrostatic pulling of polypeptides is a process that adds to the complexity of the energetic landscape associated with the electrophoretic insertion accomplished by the transmembrane voltage (4–13). …”

Section: Introductionmentioning

confidence: 99%

Facilitated translocation of polypeptides through a single nanopore

Bikwemu

Wolfe

Xing

et al. 2010

J. Phys.: Condens. Matter

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The transport of polypeptides through nanopores is a key process in biology and medical biotechnology. Despite its critical importance, the underlying kinetics of polypeptide translocation through protein nanopores is not yet comprehensively understood. Here, we present a simple two-barrier, one-well kinetic model for the translocation of short positively charged polypeptides through a single transmembrane protein nanopore that is equiped with negatively charged rings, simply called traps. We demonstrate that the presence of these traps within the interior of the nanopore dramatically alters the free energy landscape for the partitioning of the polypeptide into the nanopore interior, as revealed by significant modifications in the activation free energies required for the transitions of the polypeptide from one state to other. Our kinetic model permits the calculation of the relative and absolute exit frequencies of the short cationic polypeptides through either opening of the nanopore. Moreover, this approach enabled quantitative assessment of the kinetics of translocation of the polypeptides through a protein nanopore, which is strongly dependent on several factors, including the nature of the translocating polypeptide, the position of the traps, the strength of the polypeptide-attractive trap interactions and the applied transmembrane voltage.

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“…Although some universal features of the translocation process can be analyzed by means of suitably simplified statistical models [7,8,9,10], and non-hydrodynamic coarse-grained or microscopic models [11,12,13,14], a quantitative description of this complex phenomenon calls for realistic, stateof-the-art computational modeling. Work along these lines has been recently reported by several groups, beginning with the first multiscale simulations by the present authors [15,16], followed by Langevin dynamics simulations [17] and more recently by coupled molecular-fluid dynamics [18,20].…”

Section: Introductionmentioning

confidence: 99%

Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: Theory and multiscale simulations

et al. 2008

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We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power law dependence of the translocation time on the polymer length with an exponent α ≈ 1.2. The actual value of the exponent from the simulations is α = 1.28 ± 0.01, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.

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Translocation of polymers with folded configurations across nanopores

Cited by 17 publications

References 45 publications

The Passage of Homopolymeric RNA through Small Solid‐State Nanopores

The Passage of Homopolymeric RNA through Small Solid‐State Nanopores

Facilitated translocation of polypeptides through a single nanopore

Hydrodynamic correlations in the translocation of a biopolymer through a nanopore: Theory and multiscale simulations

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