Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor

Nature Communications

Volumn 4, Issue , 2013, Pages

  Liu, Lei ^a   Yang, Chun ^a   Zhao, Kai ^a   Li, Jingyuan ^a   Wu, Hai Chen ^a  

^a INSTITUTE OF HIGH ENERGY PHYSICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; LIPID; SINGLE STRANDED DNA; SINGLE WALLED NANOTUBE;

CARBON; DNA; GENOMICS; LIPID; MOLECULAR ANALYSIS; NANOTECHNOLOGY; SENSOR; TRANSLOCATION;

ARTICLE; CHEMICAL MODIFICATION; CONTROLLED STUDY; DNA DETERMINATION; GENE TRANSLOCATION; ION TRANSPORT; LIPID BILAYER; MOLECULAR SENSOR; NANOPORE; NANOSENSOR; NONHUMAN;

ALGORITHMS; BIOLOGICAL TRANSPORT; BIOSENSING TECHNIQUES; CYTOSINE; DNA; DNA DAMAGE; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; IONS; LIPID BILAYERS; MOLECULAR DYNAMICS SIMULATION; NANOPORES; NANOTECHNOLOGY; NANOTUBES, CARBON; THERMODYNAMICS;

EID: 84893428776     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms3989     Document Type: Article

References (46)

1. Coulter, W. H. Means for counting particles suspended in a fluid. U.S. Patent 2,656,508 (1953).
2. Kasianowicz, J. J., Brandin, E., Branton, D. & Deamer, D. W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl Acad. Sci. USA 93, 13770-13773 (1996).
3. Gu, L. Q., Braha, O., Conlan, S., Cheley, S. & Bayley, H. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter. Nature 398, 686-690 (1999).
4. Braha, O. et al. Simultaneous stochastic sensing of divalent metal ions. Nat. Biotechnol. 18, 1005-1007 (2000).
5. Movileanu, L., Howorka, S., Braha, O. & Bayley, H. Detecting protein analytes that modulate transmembrane movement of a polymer chain within a single protein pore. Nat. Biotechnol. 18, 1091-1095 (2000).
6. Li, J. et al. Ion-beam sculpting at nanometre length scales. Nature 412, 166-169 (2001).
7. Storm, A. J., Chen, J. H., Ling, X. S., Zandbergen, H. W. & Dekker, C. Fabrication of solid-state nanopores with single-nanometre precision. Nat. Mater. 2, 537-540 (2003).
8. Dekker, C. Solid-state nanopores. Nat. Nanotech. 2, 209-215 (2007).
9. Liu, H. et al. Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327, 64-67 (2010).
10. Garaj, S. et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190-193 (2010).
11. Merchant, C. A. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 2915-2921 (2010).
12. Schneider, G. F. et al. DNA translocation through graphene nanopores. Nano Lett. 10, 3163-3167 (2010).
13. Langecker, M. et al. Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338, 932-936 (2012).
14. Lee, C. Y., Choi, W., Han, J.-H. & Strano, M. S. Coherence resonance in a single-walled carbon nanotube ion channel. Science 329, 1320-1324 (2010).
15. Branco, M. R., Ficz, G. & Reik, W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat. Rev. Genet. 13, 7-13 (2012).
16. Wu, J., Gerstandt, K., Zhang, H., Liu, J. & Hinds, B. J. Electrophoretically induced aqueous flow through single-walled carbon nanotube membranes. Nat. Nanotech. 7, 133-139 (2012).
17. Clarke, J. et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotech. 4, 265-270 (2009).
18. Cherf, G. M. et al. Automated forward and reverse ratcheting of DNA in a nanopore at 5-angstrom precision. Nat. Biotechnol. 30, 344-348 (2012).
19. Manrao, E. A. et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat. Biotechnol. 30, 349-353 (2012).
20. Peter, C. & Hummer, G. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophys. J. 89, 2222-2234 (2005).
21. Henrickson, S. E., Misakian, M., Robertson, B. & Kasianowicz, J. J. Driven DNA transport into an asymmetric nanometer-scale pore. Phys. Rev. Lett. 85, 3057-3060 (2000).
22. Meller, A., Nivon, L. & Branton, D. Voltage-driven DNA translocations through a nanopore. Phys. Rev. Lett. 86, 3435-3438 (2001).
23. Skinner, G. M., van den Hout, M., Broekmans, O., Dekker, C. & Dekker, N. H. Distinguishing single- and double-stranded nucleic acid molecules using solidstate nanopores. Nano Lett. 9, 2953-2960 (2009).
24. Yeh, I. C. & Hummer, G. Nucleic acid transport through carbon nanotube membranes. Proc. Natl Acad. Sci. USA 101, 12177-12182 (2004).
25. Lulevich, V., Kim, S., Grigoropoulos, C. P. & Noy, A. Frictionless sliding of single-stranded DNA in a carbon nanotube pore observed by single molecule force spectroscopy. Nano. Lett. 11, 1171-1176 (2011).
26. Rabin, Y. & Tanaka, M. DNA in nanopores: Counterion condensation and coion depletion. Phys. Rev. Lett. 94, 148103 (2005).
27. Smeets, R. M. M. et al. Salt dependence of ion transport and DNA translocation through solid-state nanopores. Nano Lett. 6, 89-95 (2006).
28. Booth, M. J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934-937 (2012).
29. Song, C.-X. et al. Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine. Nat. Methods 9, 75-77 (2012).
30. Yu, M. et al. Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149, 1368-1380 (2012).
31. Laszlo, A. H. et al. Detection and mapping of 5-methylcytosine and 5-hydroxy-methylcytosine with nanopore MspA. Proc. Natl Acad. Sci. USA 110, 18904-18909 (2013).
32. Wanunu, M., Morrison, W., Rabin, Y., Grosberg, A. Y. & Meller, A. Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. Nat. Nanotech. 5, 160-165 (2010).
33. Wang, Y., Zheng, D. L., Tan, Q. L., Wang, M. X. & Gu, L. Q. Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat. Nanotech. 6, 668-674 (2011).
34. Wen, S. et al. Highly sensitive and selective DNA-based detection of mercury(II) with α-hemolysin nanopore. J. Am. Chem. Soc. 133, 18312-18317 (2011).
35. Mitchell, N. & Howorka, S. Chemical tags facilitate the sensing of individual DNA strands with nanopores. Angew. Chem. Int. Ed. 47, 5565-5568 (2008).
36. Butler, T. Z., Gundlach, J. H. & Troll, M. Ionic current blockades from DNA and RNA molecules in the a-hemolysin nanopore. Biophys. J. 93, 3229-3240 (2007).
37. Li, W.-W., Gong, L. & Bayley, H. Single-molecule detection of 5-hydroxymethylcytosine in DNA through chemical modification and nanopore analysis. Angew. Chem. Int. Ed. 52, 4350-4355 (2013).
38. Li, X. et al. Selective synthesis combined with chemical separation of single-walled carbon nanotubes for chirality selection. J. Am. Chem. Soc. 129, 15770-15771 (2007).
39. Tu, X., Manohar, S., Jagota, A. & Zheng, M. DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes. Nature 460, 250-253 (2009).
40. Holt, J. K. et al. Fast mass transport through sub-2-nanometer carbon nanotubes. Science 312, 1034-1037 (2006).
41. Iijima, S. & Ichihashi, T. Single-shell carbon nanotubes of 1-nm diameter. Nature 363, 603-605 (1993).
42. Islam, M. F., Milkie, D. E., Torrens, O. N., Yodh, A. G. & Kikkawa, J. M. Magnetic heterogeneity and alignment of single wall carbon nanotubes. Phys. Rev. B 71, 201401 (2005).
43. Liu, J. et al. Fullerene pipes. Science 280, 1253-1256 (1998).
44. Huang, X. Y., McLean, R. S. & Zheng, M. High-resolution length sorting and purification of DNA-wrapped carbon nanotubes by size-exclusion chromatography. Anal. Chem. 77, 6225-6228 (2005).
45. Holden, M. A. & Bayley, H. Direct introduction of single protein channels and pores into lipid bilayers. J. Am. Chem. Soc. 127, 6502-6503 (2005).
46. Holden, M. A., Jayasinghe, L., Daltrop, O., Mason, A. & Bayley, H. Direct transfer of membrane proteins from bacteria to planar bilayers for rapid screening by single-channel recording. Nat. Chem. Biol. 2, 314-318 (2006).