Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores

Han-Xian Hu; Fan Wu; Xiao Yang; Chao Wang; Meng-Bo Luo

doi:10.1007/s10118-022-2696-2

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Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores

RESEARCH ARTICLE | Updated：2022-04-26

- Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores
- Chinese Journal of Polymer Science Vol. 40, Issue 5, Pages: 532-540(2022)
- Affiliations：
  
  a.Department of Physics, Zhejiang University, Hangzhou 310027, China
  b.Department of Physics, Taizhou University, Taizhou 318000, China
- Author bio：
  
  luomengbo@zju.edu.cn
- Funds：
- DOI：10.1007/s10118-022-2696-2
  CLC：
- Received：06 December 2021，
  
  Revised：2022-1-6，
  
  Accepted：14 January 2022，
  
  Online First：17 March 2022，
  
  Published：01 May 2022
- Accepted：
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Hu, H. X.; Wu, F.; Yang, X.; Wang, C.; Luo, M. B. Effect of solvent viscosity on the driven translocation of charged polymers through nanopores. Chinese J. Polym. Sci. 2022, 40, 532–540

Han-Xian Hu, Fan Wu, Xiao Yang, et al. Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores[J]. Chinese Journal of Polymer Science, 2022, 40(5): 532-540.
Hu, H. X.; Wu, F.; Yang, X.; Wang, C.; Luo, M. B. Effect of solvent viscosity on the driven translocation of charged polymers through nanopores. Chinese J. Polym. Sci. 2022, 40, 532–540 DOI： 10.1007/s10118-022-2696-2.

Han-Xian Hu, Fan Wu, Xiao Yang, et al. Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores[J]. Chinese Journal of Polymer Science, 2022, 40(5): 532-540. DOI： 10.1007/s10118-022-2696-2.

摘要

Abstract

The effect of viscosity of non-translocated (

cis

) side

cis

on the driven translocation of charged polymers through nanopores is investigated using Langevin dynamics simulation. Results show that the translocation of polymer chains can be regulated by changing

cis

. As

cis

decreases

the translocation time

decreases

and the exponent

in the scaling relation with driving force

−

increases whereas

in the scaling relation with chain length

decreases. Simultaneously

the conformation of the polymer chain at the

cis

side gravitates towards an equilibrium state. The results imply a relationship between the translocation and the conformation of polymer chains. To verify this hypothesis

we change the conformation of polymer by artificially relaxing the translocating polymer

via

adding an additional relaxation time in the simulation. A sufficient large additional relaxation time for the translocating polymer chain at the

cis

side only or at both

cis

and

trans

sides results in exponents

and

both close to 1

in contrast to

=1.36 and

=0.8 for the translocation without the additional relaxation. The additional relaxation for the polymer chain at the

cis

side accelerates the translocation and plays a more important role than that for polymer chain at the

trans

side.

关键词

Keywords

references

Kasianowicz, J. J.; Brandin, E.; Branton, D.; Deamer, D. W . Characterization of individual polynucleotide molecules using a membrane channel . Proc. Natl. Acad. Sci. U. S. A. , 1996 . 93 13770 - 13773 . DOI: 10.1073/pnas.93.24.13770 http://doi.org/10.1073/pnas.93.24.13770 .

Han, J.; Turner, S. W.; Craighead, H. G . Entropic trapping and escape of long DNA molecules at submicron size constriction . Phys. Rev. Lett. , 1999 . 83 1688 - 1691 . DOI: 10.1103/PhysRevLett.83.1688 http://doi.org/10.1103/PhysRevLett.83.1688 .

Meller, A.; Nivon, L.; Branton, D . Voltage-driven DNA translocations through a nanopore . Phys. Rev. Lett. , 2001 . 86 3435 - 3438 . DOI: 10.1103/PhysRevLett.86.3435 http://doi.org/10.1103/PhysRevLett.86.3435 .

Storm, A. J.; Storm, C.; Chen, J. H.; Zandbergen, H.; Joanny, J. F.; Dekker, C . Fast DNA translocation through a solid-state nanopore . Nano Lett. , 2005 . 5 1193 - 1197 . DOI: 10.1021/nl048030d http://doi.org/10.1021/nl048030d .

Dubbeldam, J. L. A.; Rostiashvili, V. G.; Milchev, A.; Vilgis, T. A . Forced translocation of a polymer: dynamical scaling versus molecular dynamics simulation . Phys. Rev. E , 2012 . 85 041801 .

Suhonen, P. M.; Piili, J.; Linna, R. P . Quantification of tension to explain bias dependence of driven polymer translocation dynamics . Phys. Rev. E , 2017 . 96 062401 DOI: 10.1103/PhysRevE.96.062401 http://doi.org/10.1103/PhysRevE.96.062401 .

Sarabadani, J.; Ala Nissila, T . Theory of pore-driven and end-pulled polymer translocation dynamics through a nanopore: an overview . J. Phys.: Condens. Matter , 2018 . 30 274002 DOI: 10.1088/1361-648X/aac796 http://doi.org/10.1088/1361-648X/aac796 .

Suhonen, P. M.; Linna, R. P . Dynamics of driven translocation of semiflexible polymers . Phys. Rev. E , 2018 . 97 062413 DOI: 10.1103/PhysRevE.97.062413 http://doi.org/10.1103/PhysRevE.97.062413 .

Simon, S. M.; Blobel, G . A protein-conducting channel in the endoplasmic reticulum . Cell , 1991 . 65 371 - 380 . DOI: 10.1016/0092-8674(91)90455-8 http://doi.org/10.1016/0092-8674(91)90455-8 .

Bayley, H . Sequencing single molecules of DNA . Curr. Opin. Chem. Biol. , 2006 . 10 628 - 637 . DOI: 10.1016/j.cbpa.2006.10.040 http://doi.org/10.1016/j.cbpa.2006.10.040 .

Derrington, I. M.; Butler, T. Z.; Collins, M. D.; Manrao, E.; Pavlenok, M.; Niederweis, M.; Gundlach, J. H . Nanopore DNA sequencing with MspA . Proc. Natl. Acad. Sci. U. S. A. , 2010 . 107 16060 - 16065 . DOI: 10.1073/pnas.1001831107 http://doi.org/10.1073/pnas.1001831107 .

Venkatesan, B. M.; Bashir, R . Nanopore sensors for nucleic acid analysis . Nat. Nanotechnol. , 2011 . 6 615 - 624 . DOI: 10.1038/nnano.2011.129 http://doi.org/10.1038/nnano.2011.129 .

Kumar, S.; K. Agrawal, Y . Progresses in nanopores fabrications and nanopore sequencing . Nanosci. Nanotechol.-Asia , 2011 . 1 2 - 13 . .

Ying, Y. L.; Zhang, J.; Gao, R.; Long, Y. T . Nanopore-based sequencing and detection of nucleic acids . Angew. Chem. Int. Ed. , 2013 . 52 13154 - 13161 . DOI: 10.1002/anie.201303529 http://doi.org/10.1002/anie.201303529 .

Shi, X.; Li, Q.; Gao, R.; Si, W.; Liu, S. C.; Aksimentiev, A.; Long, Y. T . Dynamics of a molecular plug docked onto a solid-state nanopore . J. Phys. Chem. Lett. , 2018 . 9 4686 - 4694 . DOI: 10.1021/acs.jpclett.8b01755 http://doi.org/10.1021/acs.jpclett.8b01755 .

Yu, W. C . Translocation of heterogeneous flexible polymers assisted by binding particles . Chinese J. Polym. Sci. , 2020 . 38 784 - 790 . DOI: 10.1007/s10118-020-2387-9 http://doi.org/10.1007/s10118-020-2387-9 .

Meller, A . Dynamics of polynucleotide transport through nanometre-scale pores . J. Phys.: Condens. Matter , 2003 . 15 R581 - R607 . DOI: 10.1088/0953-8984/15/17/202 http://doi.org/10.1088/0953-8984/15/17/202 .

Chen, P.; Gu, J. J.; Brandin, E.; Kim, Y . R.; Wang, Q.; Branton, D. Probing single DNA molecule transport using fabricated nanopores . Nano Lett. , 2004 . 4 2293 - 2298 . DOI: 10.1021/nl048654j http://doi.org/10.1021/nl048654j .

Meller, A.; Branton, D . Single molecule measurements of DNA transport through a nanopore . Electrophoresis , 2002 . 23 2583 - 2591 . DOI: 10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H http://doi.org/10.1002/1522-2683(200208)23:16<2583::AID-ELPS2583>3.0.CO;2-H .

Milchev, A . Single-polymer dynamics under constraints: scaling theory and computer experiment . J. Phys.: Condens. Matter , 2011 . 23 103101 DOI: 10.1088/0953-8984/23/10/103101 http://doi.org/10.1088/0953-8984/23/10/103101 .

Sung, W.; Park, P. J . Polymer translocation through a pore in a membrane . Phys. Rev. Lett. , 1996 . 77 783 - 786 . DOI: 10.1103/PhysRevLett.77.783 http://doi.org/10.1103/PhysRevLett.77.783 .

Muthukumar, M . Polymer translocation through a hole . J. Chem. Phys. , 1999 . 111 10371 - 10374 . DOI: 10.1063/1.480386 http://doi.org/10.1063/1.480386 .

Polson, J. M.; McCaffrey, A. C. M . Polymer translocation dynamics in the quasi-static limit . J. Chem. Phys. , 2013 . 138 174902 DOI: 10.1063/1.4803022 http://doi.org/10.1063/1.4803022 .

Chuang, J.; Kantor, Y.; Kardar, M . Anomalous dynamics of translocation . Phys. Rev. E , 2001 . 65 011802 .

Kantor, Y.; Kardar, M . Anomalous dynamics of forced translocation . Phys. Rev. E , 2004 . 69 021806 DOI: 10.1103/PhysRevE.69.021806 http://doi.org/10.1103/PhysRevE.69.021806 .

Sakaue, T . Nonequilibrium dynamics of polymer translocation and straightening . Phys. Rev. E , 2007 . 76 021803 .

Rowghanian, P.; Grosberg, A. Y . Force-driven polymer translocation through a nanopore: an old problem revisited . J. Phys. Chem. B , 2011 . 115 14127 - 14135 . .

Sarabadani, J.; Ikonen, T.; Ala-Nissila, T . Iso-flux tension propagation theory of driven polymer translocation: the role of initial configurations . J. Chem. Phys. , 2014 . 141 214907 DOI: 10.1063/1.4903176 http://doi.org/10.1063/1.4903176 .

Wu, F.; Fu, Y.; Yang, X.; Sun, L. Z.; Luo, M. B . Driven translocation of semiflexible polyelectrolyte through a nanopore . J. Polym. Sci. Part B: Polym. Phys. , 2019 . 57 912 - 921 . DOI: 10.1002/polb.24846 http://doi.org/10.1002/polb.24846 .

Dubbeldam, J. L. A.; Milchev, A.; Rostiashvili, V. G.; Vilgis, T. A . Polymer translocation through a nanopore: a showcase of anomalous diffusion . Phys. Rev. E , 2007 . 76 010801 DOI: 10.1103/PhysRevE.76.010801 http://doi.org/10.1103/PhysRevE.76.010801 .

Luo, K.; Ala Nissila, T.; Ying, S. C.; Metzler, R . Driven polymer translocation through nanopores: slow-vs.-fast dynamics . EPL , 2009 . 88 68006 DOI: 10.1209/0295-5075/88/68006 http://doi.org/10.1209/0295-5075/88/68006 .

Sakaue, T . Sucking genes into pores: insight into driven translocation . Phys. Rev. E , 2010 . 81 041808 DOI: 10.1103/PhysRevE.81.041808 http://doi.org/10.1103/PhysRevE.81.041808 .

Sarabadani, J.; Ikonen, T.; Mokkonen, H.; Ala-Nissila, T.; Carson, S.; Wanunu, M . Driven translocation of a semi-flexible polymer through a nanopore . Sci. Rep. , 2017 . 7 7423 DOI: 10.1038/s41598-017-07227-3 http://doi.org/10.1038/s41598-017-07227-3 .

Vocks, H.; Panja, D.; Barkema, G. T.; Ball, R. C . Pore-blockade times for field-driven polymer translocation . J. Phys.: Condens. Matter , 2008 . 20 095224 DOI: 10.1088/0953-8984/20/9/095224 http://doi.org/10.1088/0953-8984/20/9/095224 .

Carson, S.; Wilson, J.; Aksimentiev, A.; Wanunu, M . Smooth DNA transport through a narrowed pore geometry . Biophys. J. , 2014 . 107 2381 - 2393 . DOI: 10.1016/j.bpj.2014.10.017 http://doi.org/10.1016/j.bpj.2014.10.017 .

Luo, K.; Metzler, R . Polymer translocation into a fluidic channel through a nanopore . Phys. Rev. E , 2010 . 82 021922 DOI: 10.1103/PhysRevE.82.021922 http://doi.org/10.1103/PhysRevE.82.021922 .

Kwon, S.; Sung, B. J . Effects of solvent quality and non-equilibrium conformations on polymer translocation . J. Chem. Phys. , 2018 . 149 244907 DOI: 10.1063/1.5048059 http://doi.org/10.1063/1.5048059 .

Liang, J.; Wei, H.; Yu, K.; Lin, C.; Li, H.; Ding, M.; Duan, X . Structure and dynamics of ions in dipolar solvents: a coarse-grained simulation study . Soft Matter , 2021 . 17 6305 - 6314 . DOI: 10.1039/D1SM00583A http://doi.org/10.1039/D1SM00583A .

Weeks, J. D.; Chandler, D.; Andersen, H. C . Role of repulsive forces in determining equilibrium structure of simple liquids . J. Chem. Phys. , 1971 . 54 5237 - 5247 . DOI: 10.1063/1.1674820 http://doi.org/10.1063/1.1674820 .

Duan, X.; Shi, A. C.; An, L . Formation of ionomer microparticles via polyelectrolyte complexation . Macromolecules , 2021 . 54 9053 - 9062 . DOI: 10.1021/acs.macromol.1c01400 http://doi.org/10.1021/acs.macromol.1c01400 .

Alapati, S.; Fernandes, D. V.; Suh, Y. K . Numerical and theoretical study on the mechanism of biopolymer translocation process through a nano-pore . J. Chem. Phys. , 2011 . 135 055103 DOI: 10.1063/1.3622490 http://doi.org/10.1063/1.3622490 .

Fyta, M . G.; Melchionna, S.; Kaxiras, E.; Succi, S. Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore . Multiscale Model. Simul. , 2006 . 5 1156 - 1173 . DOI: 10.1137/060660576 http://doi.org/10.1137/060660576 .

Zhang, Y.; Zhou, H.; Ou-Yang, Z. C . Stretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions . Biophys. J. , 2001 . 81 1133 - 1143 . DOI: 10.1016/S0006-3495(01)75770-0 http://doi.org/10.1016/S0006-3495(01)75770-0 .

Dessinges, M . N.; Maier, B.; Zhang, Y.; Peliti, M.; Bensimon, D.; Croquette, V. Stretching single stranded DNA, a model polyelectrolyte . Phys. Rev. Lett. , 2002 . 89 248102 DOI: 10.1103/PhysRevLett.89.248102 http://doi.org/10.1103/PhysRevLett.89.248102 .

Chodanowski, P.; Stoll, S . Polyelectrolyte adsorption on charged particles in the Debye-Hückel approximation. a Monte Carlo approach . Macromolecules , 2001 . 34 2320 - 2328 . DOI: 10.1021/ma000482z http://doi.org/10.1021/ma000482z .

Duan, X.; Zhang, Y.; Li, L.; Zhang, R.; Ding, M.; Huang, Q.; Xu, W . S.; Shi, T.; An, L. Effects of concentration and ionization degree of anchoring cationic polymers on the lateral heterogeneity of anionic lipid monolayers . J. Phys. Chem. B , 2017 . 121 984 - 994 . DOI: 10.1021/acs.jpcb.6b12386 http://doi.org/10.1021/acs.jpcb.6b12386 .

Luo, M. B . Translocation of polymer through nanopore: dissipative particle dynamics simulation . Chin. Sci. Bull. , 2014 . 59 4960 - 4967 . DOI: 10.1007/s11434-014-0621-y http://doi.org/10.1007/s11434-014-0621-y .

Luo, M. B.; Tsehay, D. A.; Sun, L. Z . Temperature dependence of the translocation time of polymer through repulsive nanopores . J. Chem. Phys. , 2017 . 147 034901 DOI: 10.1063/1.4993217 http://doi.org/10.1063/1.4993217 .

Adhikari, R.; Bhattacharya, A . Effect of solvent viscosity on driven translocation of a semi-flexible chain through a nano-pore . EPL , 2018 . 121 68006 DOI: 10.1209/0295-5075/121/68006 http://doi.org/10.1209/0295-5075/121/68006 .

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