Elucidating the dynamics of polymer transport through nanopores using asymmetric salt concentrations

Charron, Martin; Philipp, Lucas; He, Liqun; Tabard‐Cossa, Vincent

doi:10.1007/s12274-022-4886-3

Cited by 7 publications

(7 citation statements)

References 80 publications

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“…The pulley effect has been observed by others in experiments and simulations since then. 14,41,42 A challenge in utilizing this mechanism to promote singlefile capture is the dominance of drift over diffusion in stronger flows. In other words, one could increase the pressure difference to have a stronger velocity gradient, thereby enhancing the forces driving the pulley effect, but consequently, the polymer is carried away with the flow and arrives at the pore faster before significant unraveling takes place.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

2023

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Solid-state nanopore sensors remain a promising solution to the rising global demand for genome sequencing. These single-molecule sensing technologies require single-file translocation for high resolution and accurate detection. In a previous publication, we discovered a hairpin unraveling mechanism, namely, the pulley effect, in a pressure-driven translocation system. In this paper, we further investigate the pulley effect in the presence of pressure-driven fluid flow and an opposing force provided by an electrostatic field as an approach to increase single-file capture probability. A hydrodynamic flow is used to move the polymer forward, and two oppositely charged electrostatic square loops are used to create an opposing force. By optimizing the balance between forces, we show that the single-file capture can be amplified from about 50% to almost 95%. The force location, force strength, and flow rate are used as the optimizing variables.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

2023

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“…The translocation time also increases if the concentration of the counterions is increased in the solution [ 231 ], which, however, leads to a reduced capture rate. Creating an ionic gradient across the pore might remedy this issue and increase the capture rate; having a lower salt concentration on the cis side increases the capture rate without decreasing the translocation time [ 124 , 236 , 237 , 238 , 239 , 240 ]. Increasing the viscosity of the solvent again reduces the mobility of the DNA strands, resulting in longer translocation times.…”

Section: Controlling the Speed Of Translocationmentioning

confidence: 99%

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

Singh

Chauhan

Bharadwaj

et al. 2023

IJMS

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Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

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“…The electric field gradient outside of the nanopore can cause both dsDNA and 3HB to approach the pore by an end: for dsDNA, the field gradient stretches out and "unwraps" the polymer as it approaches since the field pulls on the parts of dsDNA that are closer to the pore significantly more than those that are distant. [54][55][56][57][58] For the rigid 3HB molecules, the gradient results in a torque that aligns the 3HB with the field lines. 51,59,60 Similar effects have been seen for rigid molecules in other nanofluidic devices.…”

Section: Folded Fractionmentioning

confidence: 99%

DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield

Charron

Karau

et al. 2023

Nanoscale

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Elucidating the dynamics of polymer transport through nanopores using asymmetric salt concentrations

Cited by 7 publications

References 80 publications

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

Enhanced Pulley Effect for Translocation: The Interplay of Electrostatic and Hydrodynamic Forces

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges

DNA origami characterized via a solid-state nanopore: insights into nanostructure dimensions, rigidity and yield

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