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Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures

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Abstract

The emergence of MoS2 nanopores has provided a new avenue for high performance DNA sequencing, which is critical for modern chemical/biological research and applications. Herein, molecular dynamics simulations were performed to design a conceptual device to sequence DNA with MoS2 nanopores of different structures (e.g., pore rim contained Mo atoms only, S atoms only, or both Mo and S atoms), where various unfolded single-stranded DNAs (ssDNAs) translocated through the nanopores driven by transmembrane bias; the sequence content was identified by the associating ionic current. All ssDNAs adsorbed onto the MoS2 surface and translocated through the nanopores by transmembrane electric field in a stepwise manner, where the pause between two permeation events was long enough for the DNA fragments in the nanopore to produce well-defined ionic blockage current to deduce the DNA’s base sequence. The transmembrane bias and DNA-MoS2 interaction could regulate the speed of the translocation process. Furthermore, the structure (atom constitution of the nanopore rim) of the nanopore considerably regulated both the translocate process and the ionic current. Thus, MoS2 nanopores could be employed to sequence DNA with the flexibility to regulate the translocation process and ionic current to yield the optimal sequencing performance.

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References

  1. Ying Y L, Long Y T. Nanopore-based single-biomolecule interfaces: from information to knowledge. Journal of the American Chemical Society, 2019, 141(40): 15720–15729

    Article  CAS  PubMed  Google Scholar 

  2. Ameur A, Kloosterman W P, Hestand M S. Single-molecule sequencing: towards clinical applications. Trends in Biotechnology, 2019, 37(1): 72–85

    Article  CAS  PubMed  Google Scholar 

  3. Varongchayakul N, Song J, Meller A, Grinstaff M W. Single-molecule protein sensing in a nanopore: a tutorial. Chemical Society Reviews, 2018, 47(23): 8512–8524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Keyser U F. Enhancing nanopore sensing with DNA nanotechnology. Nature Nanotechnology, 2016, 11(2): 106–108

    Article  CAS  PubMed  Google Scholar 

  5. Shi W, Friedman A K, Baker L A. Nanopore sensing. Analytical Chemistry, 2017, 89(1): 157–188

    Article  CAS  PubMed  Google Scholar 

  6. Ying Y, Gao R, Hu Y, Long Y. Electrochemical confinement effects for innovating new nanopore sensing mechanisms. Small Methods, 2018, 2(6): 1700390

    Article  Google Scholar 

  7. Cao C, Ying Y L, Hu Z L, Liao D F, Tian H, Long Y T. Discrimination of oligonucleotides of different lengths with a wildtype aerolysin nanopore. Nature Nanotechnology, 2016, 11(8): 713–718

    Article  CAS  PubMed  Google Scholar 

  8. Cao C, Liao D F, Yu J, Tian H, Long Y T. Construction of an aerolysin nanopore in a lipid bilayer for single-oligonucleotide analysis. Nature Protocols, 2017, 12(9): 1901–1911

    Article  CAS  PubMed  Google Scholar 

  9. Soni G V, Dekker C. Detection of nucleosomal substructures using solid-state nanopores. Nano Letters, 2012, 12(6): 3180–3186

    Article  CAS  PubMed  Google Scholar 

  10. Li J, Tang Z P, Hu R, Fu Q, Yan E F, Wang S Y, Guo P X, Zhao Q, Yu D P. Probing surface hydrophobicity of individual protein at single-molecule resolution using solid-state nanopores. Science China Materials, 2015, 58(6): 455–466

    Article  CAS  Google Scholar 

  11. Lee K, Park K B, Kim H J, Yu J S, Chae H, Kim H M, Kim K B. Recent progress in solid-state nanopores. Advanced Materials, 2018, 30(42): e1704680

    Article  PubMed  Google Scholar 

  12. Hu R, Zhu H. Graphene-based membranes for organic solvent nanofiltration. Science China Materials, 2018, 61(3): 429–431

    Article  CAS  Google Scholar 

  13. Siwy Z S, Davenport M. Graphene opens up to DNA. Nature Nanotechnology, 2010, 5(10): 697–698

    Article  CAS  PubMed  Google Scholar 

  14. Branton D, Deamer D W, Marziali A, Bayley H, Benner S A, Butler T, Di Ventra M, Garaj S, Hibbs A, Huang X, et al. The potential and challenges of nanopore sequencing. Nature Biotechnology, 2008, 26 (10): 1146–1153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Schneider G F, Kowalczyk S W, Calado V E, Pandraud G, Zandbergen H W, Vandersypen L M, Dekker C. DNA translocation through graphene nanopores. Nano Letters, 2010, 10(8): 3163–3167

    Article  CAS  PubMed  Google Scholar 

  16. Wilson J, Sloman L, He Z, Aksimentiev A. Graphene nanopores for protein sequencing. Advanced Functional Materials, 2016, 26(27): 4830–4838

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Heerema S J, Dekker C. Graphene nanodevices for DNA sequencing. Nature Nanotechnology, 2016, 11(2): 127–136

    Article  CAS  PubMed  Google Scholar 

  18. Traversi F, Raillon C, Benameur S M, Liu K, Khlybov S, Tosun M, Krasnozhon D, Kis A, Radenovic A. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nature Nanotechnology, 2013, 8(12): 939–945

    Article  CAS  PubMed  Google Scholar 

  19. Liu K, Feng J, Kis A, Radenovic A. Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation. ACS Nano, 2014, 8(3): 2504–2511

    Article  CAS  PubMed  Google Scholar 

  20. Farimani A B, Min K, Aluru N R. DNA base detection using a single-layer MoS2. ACS Nano, 2014, 8(8): 7914–7922

    Article  CAS  PubMed  Google Scholar 

  21. Feng J, Liu K, Bulushev R D, Khlybov S, Dumcenco D, Kis A, Radenovic A. Identification of single nucleotides in MoS2 nanopores. Nature Nanotechnology, 2015, 10(12): 1070–1076

    Article  CAS  PubMed  Google Scholar 

  22. Arjmandi-Tash H, Belyaeva L A, Schneider G F. Single molecule detection with graphene and other two-dimensional materials: nanopores and beyond. Chemical Society Reviews, 2016, 45(3): 476–493

    Article  CAS  PubMed  Google Scholar 

  23. Husale B S, Sahoo S, Radenovic A, Traversi F, Annibale P, Kis A. ssDNA binding reveals the atomic structure of graphene. Langmuir, 2010, 26(23): 18078–18082

    Article  CAS  PubMed  Google Scholar 

  24. Radisavljevic B, Radenovic A, Brivio J, Giacometti V, Kis A. Single-layer MoS2 transistors. Nature Nanotechnology, 2011, 6(3): 147–150

    Article  CAS  PubMed  Google Scholar 

  25. Feng J, Liu K, Graf M, Lihter M, Bulushev R D, Dumcenco D, Alexander D T, Krasnozhon D, Vuletic T, Kis A, Radenovic A. Electrochemical reaction in single layer MoS2: nanopores opened atom by atom. Nano Letters, 2015, 15(5): 3431–3438

    Article  CAS  PubMed  Google Scholar 

  26. Heiranian M, Farimani A B, Aluru N R. Water desalination with a single-layer MoS2 nanopore. Nature Communications, 2015, 6(1): 8616

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Heckl W M, Smith D P, Binnig G, Klagges H, Hänsch T W, Maddocks J. Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy. Proceedings of the National Academy of Sciences of the United States of America, 1991, 88(18): 8003–8005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Liang L, Shen J W, Zhang Z, Wang Q. DNA sequencing by two-dimensional materials: as theoretical modeling meets experiments. Biosensors & Bioelectronics, 2017, 89(Pt 1): 280–292

    Article  CAS  Google Scholar 

  29. Sathe C, Zou X Q, Leburton J P, Schulten K. Computational investigation of DNA detection using graphene nanopores. ACS Nano, 2011, 5(11): 8842–8851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Chen H, Li L, Zhang T, Qiao Z W, Tang J, Zhou J. Protein translocation through a MoS2 nanopore: a molecular dynamics study. Journal of Physical Chemistry C, 2018, 122(4): 2070–2080

    Article  CAS  Google Scholar 

  31. Xu Z, Zhang S, Weber J K, Luan B, Zhou R, Li J. Sequential protein unfolding through a carbon nanotube pore. Nanoscale, 2016, 8(24): 12143–12151

    Article  CAS  PubMed  Google Scholar 

  32. Luan B, Zhou R. Spontaneous transport of single-stranded DNA through graphene-MoS2 heterostructure nanopores. ACS Nano, 2018, 12(4): 3886–3891

    Article  CAS  PubMed  Google Scholar 

  33. Heerema S J, Schneider G F, Rozemuller M, Vicarelli L, Zandbergen H W, Dekker C. 1/f noise in graphene nanopores. Nanotechnology, 2015, 26(7): 074001

    Article  CAS  PubMed  Google Scholar 

  34. Zhou W Q, Qiu H, Guo Y F, Guo W L. Molecular insights into distinct detection properties of α-hemolysin, MspA, CsgG, and aerolysin nanopore sensors. Journal of Physical Chemistry B, 2020, 124(9): 1611–1618

    CAS  Google Scholar 

  35. Lin Z, Chen H, Dong J, Zhao D, Li L. Nanopore-based biomolecular detection. Progress in Chemistry, 2020, 32(5): 562–580 (in Chinese)

    Google Scholar 

  36. Deng S, Hu H, Zhuang G, Zhong X, Wang J. A strain-controlled C2N monolayer membrane for gas separation in PEMFC application. Applied Surface Science, 2018, 441: 408–414

    Article  CAS  Google Scholar 

  37. Cao L, Ren H, Miao J, Guo W, Li Y, Li G. Validation of polarizable force field parameters for nucleic acids by inter-molecular interactions. Frontiers of Chemical Science and Engineering, 2016, 10(2): 203–212

    Article  CAS  Google Scholar 

  38. Yuan L, Wu H, Zhao Y, Qin X, Li Y. Molecular simulation of the interaction mechanism between CodY protein and DNA in Lactococcus lactis. Frontiers of Chemical Science and Engineering, 2019, 13(1): 133–139

    Article  CAS  Google Scholar 

  39. Liang L J, Cui P, Wang Q, Wu T, Agren H, Tu Y Q. Theoretical study on key factors in DNA sequencing with graphene nanopores. RSC Advances, 2013, 3(7): 2445–2453

    Article  CAS  Google Scholar 

  40. Hanwell M D, Curtis D E, Lonie D C, Vandermeersch T, Zurek E, Hutchison G R. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 2012, 4(1): 17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Liang L, Hu W, Xue Z, Shen J. Theoretical study on the interaction of nucleotides on two-dimensional atomically thin graphene and molybdenum disulfide. FlatChem, 2017, 2: 8–14

    Article  CAS  Google Scholar 

  42. Jorgensen W L, Chandrasekhar J, Madura J D, Impey R W, Klein M L. Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 1983, 79(2): 926–935

    Article  CAS  Google Scholar 

  43. Hess B, Kutzner C, Van Der Spoel D, Lindahl E. Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 2008, 4(3): 435–447

    Article  CAS  PubMed  Google Scholar 

  44. MacKerell A D Jr, Bashford D, Bellott M, Dunbrack R L Jr, Evanseck J D, Field M J, Fischer S, Gao J, Guo H, Ha S, et al. Allatom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B, 1998, 102(18): 3586–3616

    Article  CAS  Google Scholar 

  45. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. Journal of Molecular Graphics & Modelling, 1996, 14(1): 33–38

    Article  CAS  Google Scholar 

  46. Feng J, Graf M, Liu K, Ovchinnikov D, Dumcenco D, Heiranian M, Nandigana V, Aluru N R, Kis A, Radenovic A. Single-layer MoS2 nanopores as nanopower generators. Nature, 2016, 536(7615): 197–200

    Article  CAS  PubMed  Google Scholar 

  47. Hess B, Bekker H, Berendsen H J, Fraaije J G. LINCS: a linear constraint solver for molecular simulations. Journal of Computational Chemistry, 1997, 18(12): 1463–1472

    Article  CAS  Google Scholar 

  48. Miyamoto S, Kollman P A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. Journal of Computational Chemistry, 1992, 13(8): 952–962

    Article  CAS  Google Scholar 

  49. Qiu H, Sarathy A, Schulten K, Leburton J P. Detection and mapping of DNA methylation with 2D material nanopores. npj 2D Materials and Applications, 2017, 1(3): 1–8

    Google Scholar 

  50. Allen M P, Tildesley D J. Computer Simulation of Liquids. 1st ed. Oxford, UK: Clarendon Press, 1987, 385–386

    Google Scholar 

  51. Darden T, York D, Pedersen L. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. Journal of Chemical Physics, 1993, 98(12): 10089–10092

    Article  CAS  Google Scholar 

  52. Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. Journal of Chemical Physics, 2007, 126(1): 014101

    Article  Google Scholar 

  53. Berendsen H J C, Postma J P M, Van Gunsteren W F, DiNola A, Haak J R. Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 1984, 81(8): 3684–3690

    Article  CAS  Google Scholar 

  54. Cheng A, Merz K M. Application of the NoséHoover chain algorithm to the study of protein dynamics. Journal of Physical Chemistry, 1996, 100(5): 1927–1937

    Article  CAS  Google Scholar 

  55. Li L B, Duan Y F, Liao S W, Ke Q, Qiao Z W, Wei Y Y. Adsorption and separation of propane/propylene on various ZIF-8 polymorphs: insights from GCMC simulations and the ideal adsorbed solution theory (IAST). Chemical Engineering Journal, 2020, 386: 123945

    Article  CAS  Google Scholar 

  56. Li L, Vorobyov I, Allen T W. Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain. Journal of Physical Chemistry B, 2008, 112(32): 9574–9587

    Article  CAS  Google Scholar 

  57. Li L B, Zhang T, Duan Y F, Wei Y Y, Dong C J, Ding L, Qiao Z W, Wang H H. Selective gas diffusion in two-dimensional MXene lamellar membranes: insights from molecular dynamics simulations. Journal of Materials Chemistry. A, Materials for Energy and Sustainability, 2018, 6(25): 11734–11742

    Article  CAS  Google Scholar 

  58. Zhao D, Li L, He D, Zhou J. Molecular dynamics simulations of conformation changes of HIV-1 regulatory protein on graphene. Applied Surface Science, 2016, 377: 324–334

    Article  CAS  Google Scholar 

  59. Barati Farimani A, Dibaeinia P, Aluru N R. DNA origami-graphene hybrid nanopore for DNA detection. ACS Applied Materials & Interfaces, 2017, 9(1): 92–100

    Article  CAS  Google Scholar 

  60. Balasubramanian R, Pal S, Joshi H, Rao A, Naik A, Varma M, Chakraborty B, Maiti P K. DNA translocation through hybrid bilayer nanopores. Journal of Physical Chemistry C, 2019, 123(18): 11908–11916

    Article  CAS  Google Scholar 

  61. Qiu H, Sarathy A, Leburton J P, Schulten K. Intrinsic stepwise translocation of stretched ssDNA in graphene nanopores. Nano Letters, 2015, 15(12): 8322–8330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Chu J, Gonzalez Lopez M, Cockroft S L, Amorin M, Ghadiri M R. Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. Angewandte Chemie International Edition, 2010, 49 (52): 10106–10109

    Article  CAS  PubMed  Google Scholar 

  63. Ling Y, Gu Z, Kang S, Luo J, Zhou R. Structural damage of a β-sheet protein upon adsorption onto molybdenum disulfide nanotubes. Journal of Physical Chemistry C, 2016, 120(12): 6796–6803

    Article  CAS  Google Scholar 

  64. Zhang J, Wu S, Ma L, Wu P, Liu J. Graphene oxide as a photocatalytic nuclease mimicking nanozyme for DNA cleavage. Nano Research, 2020, 13(2): 455–460

    Article  CAS  Google Scholar 

  65. Xu Y, Wang H, Chen B, Liu H, Zhao Y. Emerging barcode particles for multiplex bioassays. Science China Materials, 2019, 62(3): 289–324

    Article  CAS  Google Scholar 

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Acknowledgements

The financial support from the Science and Technology Key Project of Guangdong Province (No. 2020B010188002), Guangdong Natural Science Foundation (No. 2019A1515011121), Guangzhou Technology Project (No. 201804010219), the National Natural Science Foundation of China (Grant Nos. 21908046 and 22078104), Hubei Natural Science Foundation (No. 2019CFB293), Guangdong Basic and Applied Basic Research Foundation (No. 2019A1515110706), State Key Laboratory of Pulp and Paper Engineering (No. SCUT201828) and the Fundamental Research Funds for the Central Universities were gratefully acknowledged.

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Authors and Affiliations

  1. School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, 510640, China

    Daohui Zhao, Huang Chen, Zhixian Li & Libo Li

  2. School of Chemistry and Chemical Engineering, Hubei University, Wuhan, 430062, China

    Daohui Zhao, Yuqing Wang & Bei Li

  3. School of Materials Science and Hydrogen Energy, Foshan University, Foshan, 528231, China

    Chongxiong Duan

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  1. Daohui Zhao
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Correspondence to Libo Li.

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Zhao, D., Chen, H., Wang, Y. et al. Molecular dynamics simulation on DNA translocating through MoS2 nanopores with various structures. Front. Chem. Sci. Eng. 15, 922–934 (2021). https://doi.org/10.1007/s11705-020-2004-z

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  • DOI: https://doi.org/10.1007/s11705-020-2004-z

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