DNA sequencing based on physical properties at single nucleotide resolution

Document Type : Article

Authors

Lab. of Computational Nanomechanics, Department of Mechanical Engineering, Sharif University of Technology, Tehran, P.O. Box 11155-9567, Iran

Abstract

To realize objectives such as genome-based medicine, it is required to develop economical and fast methods for DNA sequencing at single-nucleotide resolution. In this paper a novel approach is developed to significantly improve efficiency of DNA sequencing based on physical differences between nucleotides. Here it is claimed that the reason for rather low resolution of sequencing based on physical differences, is the extremely nonlinear and complex dynamics of the DNA; it causes great dependence of DNA translocation with respect to detectors on initial conditions and environmental disturbances. In various sequencing, the position and orientation of nucleotides would thus be different in detection time. By decreasing signal-to-noise ratio, these different dynamics of nucleotides prevent detecting slight differences in physical properties of DNA bases. The correctness of this claim is verified by designing a sequencing nanodevice in which motion of a stretched single-stranded DNA (ssDNA) is constrained in such a way that axis of ssDNA backbone is fixed and in detection time each nucleotide lies in a fixed plane. Also nonlinear effects in ssDNA and detectors interactions are reduced as low as possible. Results indicate that under these constrained conditions, specific and distinct signal for each type of nucleotide will be generated.

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Main Subjects


1. Yan, S., Li, X., Zhang, P., et al. Direct sequencing of 20-deoxy-20-uoroarabinonucleic acid (FANA) using nanopore-induced phase-shift sequencing (NIPSS)", Chemical Science, 10(10), pp. 3110{3117 (2019). 2. Zascavage, R.R., Thorson, K., and Planz, J.V. Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing", Electrophoresis, 40(2), pp. 272{280 (2019). 3. Qiu, Y., Arcadia, C., Alibakhshi, M.A., et al. Nanopore fabrication in ultrathin HFO2 membranes for nanopore-based DNA sequencing", Biophysical Journal, 114(3), p. 179a (2018). 4. Rand, A.C., Jain, M., Eizenga, J.M., et al. Mapping DNA methylation with high-throughput nanopore sequencing", Nature Methods, 14(4), p. 411 (2017). 5. Deamer, D., Akeson, M., and Branton, D. Three decades of nanopore sequencing", Nature Biotechnology, 34(5), p. 518 (2016). 6. Fuller, C.W., Kumar, S., Porel, M., et al. Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array", Proceedings of the National Academy of Sciences, 113(19), pp. 5233{5238 (2016). 7. Castro-Wallace, S.L., Chiu, C.Y., John, K.K., et al. Nanopore DNA sequencing and genome assembly on the international space station", Scienti_c Reports, 7(1), p. 18022 (2017). 2370 F. Ebadi Jalal and H. Nejat Pishkenari/Scientia Iranica, Transactions B: Mechanical Engineering 27 (2020) 2364{2371 8. Jain, M., Koren, S., Miga, K.H., et al. Nanopore sequencing and assembly of a human genome with ultra-long reads", Nature Biotechnology, 36(4), p. 338 (2018). 9. Johnson, S.S., Zaikova, E., Goerlitz, D.S., et al. Realtime DNA sequencing in the antarctic dry valleys using the oxford nanopore sequencer", Journal of Biomolecular Techniques: JBT, 28(1), p. 2 (2017). 10. Shendure, J., Balasubramanian, S., Church, G.M., et al. DNA sequencing at 40: past, present and future", Nature, 550(7676), p. 345 (2017). 11. Fotouhi, B., Ahmadi, V., and Abasifard, M. Controlling DNA translocation speed through graphene nanopore via plasmonic _elds", Scientia Iranica, 25(3), pp. 1849{1856 (2018). 12. Fotouhi, B., Ahmadi, V., Abasifard, M., et al. Petahertz-frequency plasmons in graphene nanopore and their application to nanoparticle sensing", Scientia Iranica, Transactions F., Nanotechnology, 24(3), p. 1669 (2017). 13. Meller, A., Nivon, L., and Branton, D. Voltage-driven DNA translocations through a nanopore", Physical Review Letters, 86(15), p. 3435 (2001). 14. Wendell, D., Jing, P., Geng, J., et al. Translocation of double-stranded DNA through membrane-adapted phi29 motor protein nanopores", Nature Nanotechnology, 4(11), p. 765 (2009). 15. Manrao, E.A., Derrington, I.M., Pavlenok, M., et al. Nucleotide discrimination with DNA immobilized in the MspA nanopore", PloS One, 6(10), p. e25723 (2011). 16. Li, J., Stein, D., McMullan, C., et al. Ionbeam sculpting at nanometre length scales", Nature, 412(6843), p. 166 (2001). 17. Storm, A.J., Chen, J.H., Ling, X.S., et al. Electronbeam- induced deformations of SiO2 nanostructures", Journal of Applied Physics, 98(1), p. 014307 (2005). 18. Venkatesan, B.M., Shah, A.B., Zuo, J.M., et al. DNA sensing using nanocrystalline surface-enhanced Al2O3 nanopore sensors", Advanced Functional Materials, 20(8), pp. 1266{1275 (2010). 19. Schneider, G.F., Kowalczyk, S.W., Calado, V.E., et al. DNA translocation through graphene nanopores", Nano Letters, 10(8), pp. 3163{3167 (2010). 20. Garaj, S., Hubbard, W., Reina, A., et al. Graphene as a subnanometre trans-electrode membrane", Nature, 467(7312) p. 190 (2010). 21. Postma, H.W.C. Rapid sequencing of individual DNA molecules in graphene nanogaps", Nano Letters, 10(2), pp. 420{425 (2010). 22. Heerema, S.J. and Dekker, C. Graphene nanodevices for DNA sequencing", Nature Nanotechnology, 11(2), p. 127 (2016). 23. Storm, A.J., Chen, J.H., Ling, X.S., et al. Fabrication of solid-state nanopores with single-nanometre precision", Nature Materials, 2(8), p. 537 (2003). 24. Cao, Y., Dong, S., Liu, S., et al. Building high-throughput molecular junctions using indented graphene point contacts", Angewandte Chemie, 124(49), pp. 12394{12398 (2012). 25. Island, J.O., Holovchenko, A., Koole, M., et al. Fabrication of hybrid molecular devices using multilayer graphene break junctions", Journal of Physics: Condensed Matter, 26(47), p. 474205 (2014). 26. Min, S.K., Kim, W.Y., Cho, Y., et al. Fast DNA sequencing with a graphene-based nanochannel device", Nature Nanotechnology, 6(3), p. 162 (2011). 27. Kim, Y., Kim, K.S., Kounovsky, K.L., et al. Nanochannel con_nement: DNA stretch approaching full contour length", Lab on a Chip, 11(10), pp. 1721{ 1729 (2011). 28. Kasianowicz, J.J., Brandin, E., Branton, D., et al. Characterization of individual polynucleotide molecules using a membrane channel", Proceedings of the National Academy of Sciences, 93(24), pp. 13770{ 13773 (1996). 29. Deamer, D.W. and Branton, D. Characterization of nucleic acids by nanopore analysis", Accounts of Chemical Research, 35(10), pp. 817{825 (2002). 30. Fologea, D., Gershow, M., Ledden, B., et al. Detecting single stranded DNA with a solid state nanopore", Nano Letters, 5(10), pp. 1905{1909 (2005). 31. Schneider, G.F., Kowalczyk, S.W., Calado, V.E., et al. DNA translocation through graphene nanopores", Nano Letters, 10(8), pp. 3163{3167 (2010). 32. Zwolak, M. and Di Ventra, M. Electronic signature of DNA nucleotides via transverse transport", Nano Letters, 5(3), pp. 421{424 (2005). 33. Lagerqvist, J., Zwolak, M., and Di Ventra, M. Fast DNA sequencing via transverse electronic transport", Nano Letters, 6(4), pp. 779{782 (2006). 34. Ivanov, A.P., Instuli, E., McGilvery, C.M., et al. DNA tunneling detector embedded in a nanopore", Nano Letters, 11(1), pp. 279{285 (2010). 35. Chen, X., Rungger, I., Pemmaraju, C.D., et al. Firstprinciples study of high-conductance DNA sequencing with carbon nanotube electrodes", Physical Review B., 85(11), p. 115436 (2012). 36. Zwolak, M. and Di Ventra, M. Colloquium: Physical approaches to DNA sequencing and detection", Reviews of Modern Physics, 80(1), p. 141 (2008). 37. Lagerqvist, J., Zwolak, M., and Di Ventra, M. In- uence of the environment and probes on rapid DNA sequencing via transverse electronic transport", Biophysical Journal, 93(7), pp. 2384{2390 (2007). 38. Postma, H.W.C. Rapid sequencing of individual DNA molecules in graphene nanogaps", Nano Letters, 10(2), pp. 420{425 (2010). 39. Gracheva, M.E., Xiong, A., Aksimentiev, A., et al. Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor", Nanotechnology, 17(3), p. 622 (2006). F. Ebadi Jalal and H. Nejat Pishkenari/Scientia Iranica, Transactions B: Mechanical Engineering 27 (2020) 2364{2371 2371 40. Gracheva, M.E., Aksimentiev, A., and Leburton, J.P. Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor", Nanotechnology, 17(13), p. 3160 (2006). 41. Ohshiro, T. and Umezawa, Y. Complementary basepair- facilitated electron tunneling for electrically pinpointing complementary nucleobases", Proceedings of the National Academy of Sciences, 103(1), pp. 10{14, (2006). 42. Prasongkit, J., Grigoriev, A., Pathak, B., et al. Theoretical study of electronic transport through DNA nucleotides in a double-functionalized graphene nanogap", The Journal of Physical Chemistry C, 117(29), pp. 15421{15428 (2013). 43. He, Y., Scheicher, R.H., Grigoriev, A., et al. Enhanced DNA sequencing performance through edgehydrogenation of graphene electrodes", Advanced Functional Materials, 21(14), pp. 2674{2679 (2011). 44. Gu, L.Q., Braha, O., Conlan, S., et al. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter", Nature, 398(6729), p. 686 (1999). 45. Astier, Y., Braha, O., and Bayley, H. Toward single molecule DNA sequencing: direct identi_cation of ribonucleoside and deoxyribonucleoside 5'- monophosphates by using an engineered protein nanopore equipped with a molecular adapter", Journal of the American Chemical Society, 128(5), pp. 1705{ 1710 (2006). 46. Lee, J.W. and Meller, A. Rapid DNA sequencing by direct nanoscale reading of nucleotide bases on individual DNA chains", Perspectives in Bioanalysis, 2, pp. 245{263 (2007). 47. Keyser, U.F., Koeleman, B.N., Van Dorp, S., et al. Direct force measurements on DNA in a solid-state nanopore", Nature Physics, 2(7), p. 473 (2006). 48. Qiu, H. and Guo, W. Detecting ssDNA at singlenucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study", Applied Physics Letters, 100(8), p. 083106 (2012). 49. Qamar, S., Williams, P.M., and Lindsay, S.M. Can an atomic force microscope sequence DNA using a nanopore?", Biophysical Journal, 94(4), pp. 1233{ 1240 (2008). 50. Luan, B. and Aksimentiev, A. Control and reversal of the electrophoretic force on DNA in a charged nanopore", Journal of Physics: Condensed Matter, 22(45), pp. 454123 (2010). 51. Luan, B., Martyna, G., and Stolovitzky, G. Characterizing and controlling the motion of ssDNA in a solid-state nanopore", Biophysical Journal, 101(9), pp. 2214{2222 (2011). 52. Harris, S.A. and Laughton, C.A. A simple physical description of DNA dynamics: quasi-harmonic analysis as a route to the con_gurational entropy", Journal of Physics: Condensed Matter, 19(7), pp. 076103 (2007). 53. Peyrard, M. Nonlinear dynamics and statistical physics of DNA", Nonlinearity, 17(2), p. R1 (2004). 54. Kal_e, L., Skeel, R., Bhandarkar, M., et al. NAMD2: greater scalability for parallel molecular dynamics", Journal of Computational Physics, 151(1), pp. 283{ 312 (1999). 55. Humphrey, W., Dalke, A., and Schulten, K. VMD: visual molecular dynamics", Journal of Molecular Graphics, 14(1), pp. 33{38 (1996). 56. Lu, X.J. and Olson, W.K. 3DNA: a software package for the analysis, rebuilding and visualization of threedimensional nucleic acid structures", Nucleic Acids Research, 31(17), pp. 5108{5121 (2003). 57. MacKerell Jr, A.D., Bashford, D., Bellott, M.L.D.R., et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins", The Journal of Physical Chemistry B., 102(18), pp. 3586{3616 (1998). 58. Pu, Q., Leng, Y., Zhao, X., et al. Molecular simulations of stretching gold nanowires in solvents", Nanotechnology, 18(42), p. 424007 (2007). 59. Allen, M.P. and Tildesley, D.J., Computer Simulation of Liquids, Oxford University Press (2017). 60. Essmann, U., Perera, L., Berkowitz, M.L., et al. A smooth particle mesh Ewald method", The Journal of Chemical Physics, 103(19), pp. 8577{8593 (1995). 61. Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes", Journal of Computational Physics, 23(3), pp. 327{341 (1977). 62. Grigorescu, A.E. and Hagen, C.W. Resists for sub-20- nm electron beam lithography with a focus on HSQ: state of the art", Nanotechnology, 20(29), p. 292001 (2009).