Computational studies of DNA sequencing with solid-state nanopores: Key issues and future prospects

Frontiers in Chemistry

Volumn 2, Issue FEB, 2014, Pages

  Liang, Lijun ^a,b   Wang, Qi ^b   Ågren, Hans ^a   Tu, Yaoquan ^a  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b ZHEJIANG UNIVERSITY   (China)

Author keywords

Bio nanotechnology; Computer modeling; DNA sequencing; Graphene nanopore; Molecular simulation; Solid state nanopore; Theory

Indexed keywords

EID: 84987641951     PISSN: None     EISSN: 22962646     Source Type: Journal    
DOI: 10.3389/fchem.2014.00005     Document Type: Short Survey

References (44)

1. Aksimentiev, A., Heng, J. B., Timp, G., and Schulten, K. (2004). Microscopic kinetics of DNA translocation through synthetic nanopores. Biophys. J. 87, 2086-2097. doi: 10.1529/biophysj.104.042960
2. Avdoshenko, S. M., Nozaki, D., Gomes Da Rocha, C., González, J. W., Lee, M. H., Gutierrez, R., et al. (2013). Dynamic and electronic transport properties of DNA translocation through graphene nanopores. Nano Lett. 13, 1969-1976. doi: 10.1021/nl304735k
3. Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T., et al. (2008). The potential and challenges of nanopore sequencing. Nat. Biotechnol. 26, 1146-1153. doi: 10.1038/nbt.1495
4. Cherf, G. M., Lieberman, K. R., Rashid, H., Lam, C. E., Karplus, K., and Akeson, M. (2012). Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat. Biotechnol. 30, 344-348. doi: 10.1038/nbt.2147
5. Clarke, J., Wu, H. C., Jayasinghe, L., Patel, A., Reid, S., and Bayley, H. (2009). Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4, 265-270. doi: 10.1038/nnano.2009.12
6. Fologea, D., Uplinger, J., Thomas, B., McNabb, D. S., and Li, J. L. (2005). Slowing DNA translocation in a solid-state nanopore. Nano Lett. 5, 1734-1737. doi: 10.1021/nl051063o
7. Garaj, S., Liu, S., Golovchenko, J. A., and Branton, D. (2013). Molecule-hugging graphene nanopores. Proc. Natl. Acad. Sci. U.S.A. 110, 12192-12196. doi: 10.1073/pnas.1220012110
8. Ghosal, S. (2007). Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore. Phys. Rev. Lett. 98:238104. doi: 10.1103/PhysRevLett.98.238104
9. Gierhart, B. C., Howitt, D. G., Chen, S. J., Zhu, Z., Kotecki, D. E., Smith, R. L., et al. (2008). Nanopore with transverse nanoelectrodes for electrical characterization and sequencing of DNA. Sens. Actuators B Chem. 132, 593-600. doi: 10.1016/j.snb.2007.11.054
10. Harding, J. D., and Keller, R. A. (1992). Single-molecule detection as an approach to rapid DNA sequencing. Trends Biotechnol. 10, 55-57. doi: 10.1016/0167-7799(92)90170-Z
11. He, Y., Tsutsui, M., Scheicher, R. H., Bai, F., Taniguchi, M., and Kawai, T. (2012). Thermophoretic Manipulation of DNA translocation through nanopores. ACS Nano 7, 538-546. doi: 10.1021/nn304914j
12. Japrung, D., Henricus, M., Li, Q. H., Maglia, G., and Bayley, H. (2010). Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore. Biophys. J. 98, 1856-1863. doi: 10.1016/j.bpj.2009.12.4333
13. Kasianowicz, J. J., Brandin, E., Branton, D., and Deamer, D. W. (1996). Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. U.S.A. 93, 13770-13773. doi: 10.1073/pnas.93.24.13770
14. Kejian, D., Sun, W. M., Zhang, H. Y., Peng, X. L., and Hu, H. G. (2009). Dependence of zeta potential on polyelectrolyte moving through a solid-state nanopore. Appl. Phys. Lett. 94, 014101-014104-3. doi: 10.1063/1.3065029
15. Kowalczyk, S. W., and Dekker, C. (2012). Measurement of the docking time of a DNA molecule onto a solid-state nanopore. Nano Lett. 12, 4159-4163. doi: 10.1021/nl301719a
16. Kowalczyk, S. W., Wells, D. B., Aksimentiev, A., and Dekker, C. (2012). Slowing down DNA translocation through a nanopore in lithium chloride. Nano Lett. 12, 1038-1044. doi: 10.1021/nl204273h
17. Ku, C. S., and Roukos, D. H. (2013). From next-generation sequencing to nanopore sequencing technology: paving the way to personalized genomic medicine. Expert Rev. Med. Devices 10, 1-6. doi: 10.1586/erd.12.63
18. Liang, L., Cui, P., Wang, Q., Wu, T., Agren, H., and Tu, Y. (2013). Theoretical study on key factors in DNA sequencing with graphene nanopores. RSC Adv. 3, 2445-2453. doi: 10.1039/c2ra22109h
19. Luan, B., Afzali, A., Harrer, S., Peng, H., Waggoner, P., Polonsky, S., et al. (2010). Tribological effects on DNA translocation in a nanochannel coated with a self-assembled monolayer. J. Phys. Chem. B 114, 17172-17176. doi: 10.1021/jp108865q
20. Luan, B., and Aksimentiev, A. (2008). Electro-osmotic screening of the DNA charge in a nanopore. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 78:021912. doi: 10.1103/PhysRevE.78.021912
21. Luan, B., Wang, D., Zhou, R., Harrer, S., Peng, H., and Stolovitzky, G. (2012b). Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol. Nanotechnology 23:455102. doi: 10.1088/0957-4484/23/45/455102
22. Luan, B. Q., Stolovitzky, G., and Martyna, G. (2012a). Slowing and controlling the translocation of DNA in a solid-state nanopore. Nanoscale 4, 1068-1077. doi: 10.1039/c1nr11201e
23. Lubensky, D. K., and Nelson, D. R. (1999). Driven polymer translocation through a narrow pore. Biophys. J. 77, 1824-1838. doi: 10.1016/S0006-3495(99)77027-X
24. Maitra, R. D., Kim, J., and Dunbar, W. B. (2012). Recent advances in nanopore sequencing. Electrophoresis 33, 3418-3428. doi: 10.1002/elps.201200272
25. Manrao, E. A., Derrington, I. M., Laszlo, A. H., Langford, K. W., Hopper, M. K., Gillgren, N., et al. (2012). Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349-353. doi: 10.1038/nbt.2171
26. Merchant, C. A., Healy, K., Wanunu, M., Ray, V., Peterman, N., Bartel, J., et al. (2010). DNA Translocation through Graphene Nanopores. Nano Lett. 10, 2915-2921. doi: 10.1021/nl101046t
27. Nelson, T., Zhang, B., and Prezhdo, O. V. (2010). Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. Nano Lett. 10, 3237-3242. doi: 10.1021/nl9035934
28. Polson, J. M., and Mccaffrey, A. C. M. (2013). Polymer translocation dynamics in the quasi-static limit. J. Chem. Phys. 138, 174902-174912. doi: 10.1063/1.4803022
29. Porcu, E., Sanna, S., Fuchsberger, C., and Fritsche, L. G. (2013). Genotype imputation in genome-wide association studies. Curr. Protoc. Hum. Genet. 78, 1.25.1-1.25.14. doi: 10.1002/0471142905.hg0125s78
30. Postma, H. W. (2010). Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett. 10, 420-425. doi: 10.1021/nl9029237
31. Purnell, R. F., and Schmidt, J. J. (2009). Discrimination of single base substitutions in a DNA strand immobilized in a biological nanopore. ACS Nano 3, 2533-2538. doi: 10.1021/nn900441x
32. Pushkarev, D., Neff, N. F., and Quake, S. R. (2009). Single-molecule sequencing of an individual human genome. Nat. Biotechnol. 27, 847-850. doi: 10.1038/nbt.1561
33. Qiu, H., and Guo, W. (2012). Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: a molecular dynamics study. Appl. Phys. Lett. 100, 083106-083104. doi: 10.1063/1.3686921
34. Reimann, P., Meyer, A., and Getfert, S. (2012). On the lubensky-nelson model of polymer translocation through nanopores. Biophys. J. 103, 889-897. doi: 10.1016/j.bpj.2012.07.036
35. Rhee, M., and Burns, M. A. (2006). Nanopore sequencing technology: research trends and applications. Trends Biotechnol. 24, 580-586. doi: 10.1016/j.tibtech.2006.10.005
36. Sathe, C., Zou, X. Q., Leburton, J. P., and Schulten, K. (2011). Computational investigation of DNA detection using graphene nanopores. ACS Nano 5, 8842-8851. doi: 10.1021/nn202989w
37. Schadt, E. E., Turner, S., and Kasarskis, A. (2010). A window into third-generation sequencing. Hum. Mol. Genet. 19, R227-R240. doi: 10.1093/hmg/ddq416
38. Schneider, G. F., Kowalczyk, S. W., Calado, V. E., Pandraud, G., Zandbergen, H. W., Vandersypen, L. M. K., et al. (2010). DNA translocation through graphene nanopores. Nano Lett. 10, 3163-3167. doi: 10.1021/nl102069z
39. Venkatesan, B. M., and Bashir, R. (2011a). Nanopore sensors for nucleic acid analysis. Nat. Nanotechnol. 6, 615-624. doi: 10.1038/nnano.2011.129
40. Venkatesan, B. M., and Bashir, R. (2011b). Solid-state nanopore sensors for nucleic acid analysis. Nanopores Sens. Fund. Biol. Interact. 1-33. doi: 10.1007/978-1-4419-8252-0_1
41. Venkatesan, B. M., Dorvel, B., Yemenicioglu, S., Watkins, N., Petrov, I., and Bashir, R. (2009). Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis. Adv. Mater. 21, 2771. doi: 10.1002/adma.200803786
42. Wells, D. B., Belkin, M., Comer, J., and Aksimentiev, A. (2012). Assessing graphene nanopores for sequencing DNA. Nano Lett. 12, 4117-4123. doi: 10.1021/nl301655d
43. Yang, Y., Liu, R., Xie, H., Hui, Y., Jiao, R., Gong, Y., et al. (2013). Advances in nanopore sequencing technology. J. Nanosci. Nanotechnol. 13, 4521-4538. doi: 10.1166/jnn.2013.7756
44. Zhang, M., Yeh, L.-H., Qian, S., Hsu, J.-P., and Joo, S. W. (2012). DNA Electrokinetic translocation through a nanopore: local permittivity environment effect. J. Phys. Chem. C 116, 4793-4801. doi: 10.1021/jp211798x