Graphene nanodevices for DNA sequencing

Nature Nanotechnology

Volumn 11, Issue 2, 2016, Pages 127-136

  Heerema, Stephanie J ^a   Dekker, Cees ^a  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA SEQUENCES; GRAPHENE; NANOPORES; NANORIBBONS; NANOSTRUCTURED MATERIALS;

CREATIVE IDEAS; DISRUPTIVE INNOVATIONS; DNA SEQUENCING; EXPERIMENTAL DEMONSTRATIONS; NANO-DEVICES; NANOGAPS; PERSONALIZED MEDICINES; STRUCTURE AND PROPERTIES;

GENE ENCODING;

DNA A; GRAPHENE; IONIC LIQUID; NANOMATERIAL; NANORIBBON; GRAPHITE;

ADSORPTION; DNA SEQUENCE; MOLECULE; NANODEVICE; NANOPORE; NANOTECHNOLOGY; PRIORITY JOURNAL; REVIEW; ROOM TEMPERATURE; CHEMISTRY; DEVICES; EQUIPMENT DESIGN;

EQUIPMENT DESIGN; GRAPHITE; NANOTECHNOLOGY; SEQUENCE ANALYSIS, DNA;

EID: 84957890530     PISSN: 17483387     EISSN: 17483395     Source Type: Journal    
DOI: 10.1038/nnano.2015.307     Document Type: Review

References (130)

1. Lander E. S., et al. Initial sequencing, and analysis of the human genome. Nature 409, 860-921 (2001
2. Sanger F., Nicklen S., & Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463-5467 (1977
3. Shendure J., & Ji H. Next-generation DNA sequencing. Nature Biotechnol. 26, 1135-1145 (2008
4. Metzker M. L. Sequencing technologies -the next generation. Nature Rev. Genet. 11, 31-46 (2010
5. Ansorge W. J. Next-generation DNA sequencing techniques. New Biotechnol. 25, 195-203 (2009
6. Steinbock L. J., & Radenovic A. The emergence of nanopores in next-generation sequencing. Nanotechnology 26, 074003 (2015
7. Levene M. J., et al. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682-686 (2003
8. Quail M. A., et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences, and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012
9. Ferrarini M., et al. An evaluation of the PacBio RS platform for sequencing, and De novo assembly of a chloroplast genome. BMC Genomics 14, 670 (2013
10. Sharon D., Tilgner H., Grubert F., & Snyder M. A single-molecule long-read survey of the human transcriptome. Nature Biotechnol. 31, 1009-1014 (2013
11. Mikheyev A. S., & Tin M. M. A first look at the Oxford Nanopore MinION sequencer. Mol. Ecol. Resour. 14, 1097-1102 (2014
12. Jain M., et al. Improved data analysis for the MinION nanopore sequencer. Nature Methods 12, 351-356 (2015
13. Novoselov K. S., et al. Electric field effect in atomically thin carbon films. Science 306, 666-669 (2004
14. Novoselov K. S., et al. Two-dimensional atomic crystals. Proc. Natl Acad. Sci. USA 102, 10451-10453 (2005
15. Geim A. K., & Novoselov K. S. The rise of graphene. Nature Mater. 6, 183-191 (2007
16. Lee C., Wei X., Kysar J. W., & Hone J. Measurement of the elastic properties, and intrinsic strength of monolayer graphene. Science 321, 385-388 (2008
17. Schedin F., et al. Detection of individual gas molecules adsorbed on graphene. Nature Mater. 6, 652-655 (2007
18. Nair R. R., et al. Fine structure constant defines visual transparency of graphene. Science 320, 1308 (2008
19. Pereira V., Castro Neto A., & Peres N. Tight-binding approach to uniaxial strain in graphene. Phys. Rev. B 80, 045401 (2009
20. Balandin A. A., et Al. Superior Thermal Conductivity of Single-layer Graphene. Nano Lett. 8, 902-907 (2008
21. Morozov S., et al. Giant intrinsic carrier mobilities in graphene, and its bilayer. Phys. Rev. Lett. 100, 016602 (2008
22. Ferrari A. C., et al. Science, and technology roadmap for graphene, related two-dimensional crystals, and hybrid systems. Nanoscale 7, 4598-4810 (2015
23. Neher E., & Sakmann B. Single-channel currents recorded from membrane of denervated frog muscle fibres. Nature 260, 799-802 (1976
24. Colombini M. Pore size, and properties of channels from mitochondria isolated from Neurospora crassa. J. Membrane Biol. 53, 79-84 (1980
25. Krasilnikov O., Sabirov R., Ternovsky V., Merzliak P., & Muratkhodjaev J. A simple method for the determination of the pore radius of ion channels in planar lipid bilayer membranes. FEMS Microbiol. Lett. 105, 93-100 (1992
26. 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
27. Cherf G. M., et al. Automated forward, and reverse ratcheting of DNA in a nanopore at 5-Å precision. Nature Biotechnol. 30, 344-348 (2012
28. Manrao E. A., et al. Reading DNA at single-nucleotide resolution with a mutant MspA nanopore, and phi29 DNA polymerase. Nature Biotechnol. 30, 349-53 (2012
29. Dekker C. Solid-state nanopores. Nature Nanotech. 2, 209-215 (2007
30. Garaj S., et al. Graphene as a subnanometre trans-electrode membrane. Nature 467, 190-193 (2010
31. Garaj S., Liu S., Golovchenko J. A., & Branton D. Molecule-hugging graphene nanopores. Proc. Natl Acad. Sci. USA 110, 12192-12196 (2013
32. Sathe C., Zou X., Leburton J.-P., & Schulten K. Computational investigation of DNA detection using graphene nanopores. ACS Nano 5, 8842-8851 (2011
33. Wells D. B., Belkin M., Comer J., & Aksimentiev A. Assessing graphene nanopores for sequencing DNA. Nano Lett. 12, 4117-4123 (2012
34. Liang L., et al. Theoretical study on key factors in DNA sequencing with graphene nanopores. RSC Adv. 3, 2445-2453 (2013
35. Schneider G. F., et al. DNA translocation through graphene nanopores. Nano Lett. 10, 3163-3167 (2010
36. Merchant C. A., et al. DNA translocation through graphene nanopores. Nano Lett. 10, 2915-2921 (2010
37. Schneider G. F., et al. Tailoring the hydrophobicity of graphene for its use as nanopores for DNA translocation. Nature Commun. 4, 2619 (2013
38. Banerjee S., et al. Slowing DNA transport using graphene-DNA interactions. Adv. Funct. Mater. 25, 936-946 (2014
39. Rosenstein J. K., Wanunu M., Merchant C. A., Drndic M., & Shepard K. L. Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nature Methods 9, 487-492 (2012
40. Plesa C., van Loo N., Ketterer P., Dietz H., & Dekker C. Velocity of DNA during translocation through a solid-state nanopore. Nano Lett. 15, 732-737 (2015
41. Heerema S. J., et al. 1/f noise in graphene nanopores. Nanotechnology 26, 074001 (2015
42. Venkatesan B. M., et al. Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA, and DNA-protein complexes. ACS Nano 6, 441-450 (2012
43. Banerjee S., et al. Electrochemistry at the edge of a single graphene layer in a nanopore. ACS Nano 7, 834-843 (2013
44. Lee M.-H., et al. A low-noise solid-state nanopore platform based on a highly insulating substrate. Sci. Rep. 4, 7448 (2014
45. Postma H. W. C. Rapid sequencing of individual DNA molecules in graphene nanogaps. Nano Lett. 10, 420-425 (2010
46. Zhao Q., et al. Nanopore-based DNA analysis via graphene electrodes. J. Nanomater. 2012, 1-5 (2012
47. Zhang H., et al. Detection of nucleic acids by graphene-based devices: a first-principles study. J. Appl. Phys. 115, 133701 (2014
48. Jeong H., et al. Quantum interference in DNA bases probed by graphene nanoribbons. Appl. Phys. Lett. 103, 023701 (2013
49. Prasongkit J., Grigoriev A., Pathak B., Ahuja R., & Scheicher R. H. Transverse conductance of DNA nucleotides in a graphene nanogap from first principles. Nano Lett. 11, 1941-1945 (2011
50. Prasongkit J., Grigoriev A., Pathak B., Ahuja R., & Scheicher R. H. Theoretical study of electronic transport through DNA nucleotides in a double-functionalized graphene nanogap. J. Phys. Chem. C 117, 15421-15428 (2013
51. He Y., et al. Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes. Adv. Funct. Mater. 21, 2674-2679 (2011
52. Huang S., et al. Identifying single bases in a DNA oligomer with electron tunnelling. Nature Nanotech. 5, 868-873 (2010
53. Lindsay S., et al. Recognition tunneling. Nanotechnology 21, 262001 (2010
54. Krishnakumar P., et al. Slowing DNA translocation through a nanopore using a functionalized electrode. ACS Nano 7, 10319-10326 (2013
55. Ivanov A. P., et Al. DNA Tunneling Detector Embedded in A Nanopore. Nano Lett. 11, 279-285 (2011
56. Tsutsui M., Taniguchi M., Yokota K., & Kawai T. Identifying single nucleotides by tunnelling current. Nature Nanotech. 5, 286-290 (2010
57. Tsutsui M., et al. Single-molecule sensing electrode embedded in-plane nanopore. Sci. Rep. 1, 46 (2011
58. Bagci V. M. K., & Kaun C.-C. Recognizing nucleotides by cross-tunneling currents for DNA sequencing. Phys. Rev. E 84, 011917 (2011
59. Chen X., Rungger I., Pemmaraju C. D., Schwingenschlögl U., & Sanvito S. First principles study of high-conductance DNA sequencing with carbon nanotube electrodes. Phys. Rev. B 85, 115436 (2012
60. Prins F., et al. Room-temperature Gating of Molecular Junctions Using Few-layer Graphene Nanogap Electrodes. Nano Lett. 11, 4607-4611 (2011
61. Nef C., et al. High-yield fabrication of nm-size gaps in monolayer CVD graphene. Nanoscale 6, 7249-7254 (2014
62. Sadeghi H., et al. Conductance enlargement in picoscale electroburnt graphene nanojunctions. Proc. Natl Acad. Sci. USA 112, 2658-2663 (2015
63. Island J. O., et al. Fabrication of hybrid molecular devices using multi-layer graphene break junctions. J. Phys. Condens. Matter 26, 474205 (2014
64. Cao Y., et al. Building high-throughput molecular junctions using indented graphene point contacts. Angew. Chem. 124, 12394-12398 (2012
65. Wallace P. The band theory of graphite. Phys. Rev. 71, 622-634 (1947
66. Fujita M., Wakabayashi K., Nakada K., & Kusakabe K. Peculiar localized state at zigzag graphite edge. J. Phys. Soc. Jpn 65, 1920-1923 (1996
67. Wakabayashi K., Fujita M., Ajiki H., & Sigrist M. Electronic, and magnetic properties of nanographite ribbons. Phys. Rev. B 59, 8271-8282 (1999
68. Ezawa M. Peculiar width dependence of the electronic properties of carbon nanoribbons. Phys. Rev. B 73, 045432 (2006
69. Brey L., & Fertig H. Electronic states of graphene nanoribbons studied with the Dirac equation. Phys. Rev. B 73, 235411 (2006
70. Nakada K., Fujita M., Dresselhaus G., & Dresselhaus M. Edge state in graphene ribbons: nanometer size effect, and edge shape dependence. Phys. Rev. B 54, 17954-17961 (1996
71. Sasaki K.-i., Murakami S., & Saito R. Gauge field for edge state in graphene. J. Phys. Soc. Jpn 75, 074713 (2006
72. Nelson T., Zhang B., & Prezhdo O. V. Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device. Nano Lett. 10, 3237-3242 (2010
73. Ouyang F.-P., Peng S.-L., Zhang H., Weng L.-B., & Xu H. A biosensor based on graphene nanoribbon with nanopores: a first-principles devices-design. Chinese Phys. B 20, 058504 (2011
74. Saha K. K., Drndić M., & Nikolić B. K. DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore. Nano Lett. 12, 50-55 (2012
75. Avdoshenko S. M., et al. Dynamic, and electronic transport properties of DNA translocation through graphene nanopores. Nano Lett. 13, 1969-1976 (2013
76. Girdhar A., Sathe C., Schulten K., & Leburton J.-P. Graphene quantum point contact transistor for DNA sensing. Proc. Natl Acad. Sci. USA 110, 16748-16753 (2013
77. Ahmed T., Haraldsen J. T., Zhu J.-X., & Balatsky A. V. Next-generation epigenetic detection technique: identifying methylated cytosine using graphene nanopore. J. Phys. Chem. Lett. 5, 2601-2607 (2014
78. Sadeghi H., et al. Graphene sculpturene nanopores for DNA nucleobase sensing. J. Phys. Chem. B 118, 6908-6914 (2014
79. Ahmed T., et al. Correlation dynamics, and enhanced signals for the identification of serial biomolecules, and DNA bases. Nanotechnology 25, 125705 (2014
80. Traversi F., et al. Detecting the translocation of DNA through a nanopore using graphene nanoribbons. Nature Nanotech. 8, 939-945 (2013
81. Lu Y., Merchant C. A., Drndić M., & Johnson A. T. C. In situ electronic characterization of graphene nanoconstrictions fabricated in a transmission electron microscope. Nano Lett. 11, 5184-5188 (2011
82. Puster M., Rodríguez-Manzo J. A., Balan A., & Drndić M. Toward sensitive graphene nanoribbon-nanopore devices by preventing electron beam-induced damage. ACS Nano 7, 11283-11289 (2013
83. Qi Z. J., et Al. Correlating Atomic Structure, and Transport in Suspended Graphene Nanoribbons. Nano Lett. 14, 4238-4244 (2014
84. Song B., et al. Atomic-scale Electron-beam Sculpting of Near-defect-free Graphene Nanostructures. Nano Lett. 11, 2247-2250 (2011
85. Xu Q., et al. Controllable atomic scale patterning of freestanding monolayer graphene at elevated temperature. ACS Nano 7, 1566-1572 (2013
86. Chang P.-H., Liu H., & Nikolić B. K. First-principles versus semi-empirical modeling of global, and local electronic transport properties of graphene nanopore-based sensors for DNA sequencing. J. Comput. Electron. 13, 847-856 (2014
87. Lagerqvist J., Zwolak M., & Di Ventra M. Influence of the environment, and probes on rapid DNA sequencing via transverse electronic transport. Biophys. J. 93, 2384-2390 (2007
88. Feliciano G. T., et al. Capacitive DNA detection driven by electronic charge fluctuations in a graphene nanopore. Phys. Rev. Appl. 3, 034003 (2015
89. Jia X., Campos-Delgado J., Terrones M., Meunier V., & Dresselhaus M. S. Graphene edges: a review of their fabrication, and characterization. Nanoscale 3, 86-95 (2011
90. Qi Z. J., et al. Electronic transport of recrystallized freestanding graphene nanoribbons. ACS Nano 9, 3510-3520 (2015
91. Xie P., Xiong Q., Fang Y., Qing Q., & Lieber C. M. Local electrical potential detection of DNA by nanowire-nanopore sensors. Nature Nanotech. 7, 119-125 (2012
92. Oliveira Brett A. M., & Chiorcea A.-M. Atomic force microscopy of DNA immobilized onto a highly oriented pyrolytic graphite electrode surface. Langmuir 19, 3830-3839 (2003
93. Gowtham S., Scheicher R., Ahuja R., Pandey R., & Karna S. Physisorption of nucleobases on graphene: density-functional calculations. Phys. Rev. B 76, 033401 (2007
94. Akca S., Foroughi A., Frochtzwajg D., & Postma H. W. C. Competing interactions in DNA assembly on graphene. PLoS ONE 6, e18442 (2011
95. Lee J.-H., Choi Y.-K., Kim H.-J., Scheicher R. H., & Cho J.-H. Physisorption of DNA nucleobases on h-BN, and graphene: vdW-corrected DFT calculations. J. Phys. Chem. C 117, 13435-13441 (2013
96. Antony J., & Grimme S. Structures, and interaction energies of stacked graphene-nucleobase complexes. Phys. Chem. Chem. Phys. 10, 2722-2729 (2008
97. Varghese N., et al. Binding of DNA nucleobases, and nucleosides with graphene. ChemPhysChem 10, 206-210 (2009
98. Das A., et al. Binding of nucleobases with single-walled carbon nanotubes: theory, and experiment. Chem. Phys. Lett. 453, 266-273 (2008
99. Umadevi D., & Sastry G. N. Quantum mechanical study of physisorption of nucleobases on carbon materials: graphene versus carbon nanotubes. J. Phys. Chem. Lett. 2, 1572-1576 (2011
100. Le D., Kara A., Schröder E., Hyldgaard P., & Rahman T. S. Physisorption of nucleobases on graphene: a comparative van Der Waals study. J. Phys. Condens. Matter 24, 424210 (2012
101. Min S. K., Kim W. Y., Cho Y., & Kim K. S. Fast DNA sequencing with a graphene-based nanochannel device. Nature Nanotech. 6, 162-165 (2011
102. Cho Y., Min S. K., Kim W. Y., & Kim K. S. The origin of dips for the graphene-based DNA sequencing device. Phys. Chem. Chem. Phys. 13, 14293-14296 (2011
103. Song B., Cuniberti G., Sanvito S., & Fang H. Nucleobase adsorbed at graphene devices: enhance bio-sensorics. Appl. Phys. Lett. 100, 063101 (2012
104. Bobadilla A. D., & Seminario J. M. Assembly of a noncovalent DNA junction on graphene sheets, and electron transport characteristics. J. Phys. Chem. C 117, 26441-26453 (2013
105. Cai J., et al. Atomically precise bottom-up fabrication of graphene nanoribbons. Nature 466, 470-473 (2010
106. Ahmed T., et al. Electronic Fingerprints of DNA Bases on Graphene. Nano Lett. 12, 927-931 (2012
107. Tanaka H., & Kawai T. Partial sequencing of a single DNA molecule with a scanning tunnelling microscope. Nature Nanotech. 4, 518-522 (2009
108. Davies T. J., Hyde M. E., & Compton R. G. Nanotrench arrays reveal insight into graphite electrochemistry. Angew. Chem. Int. Ed. 44, 5121-5126 (2005
109. Bonanni A., & Pumera M. Graphene platform for hairpin-DNA-based impedimetric genosensing. ACS Nano 5, 2356-2361 (2011
110. Zainudin N., Mohd Hairul A. R., Yusoff M. M., Tan L. L., & Chong K. F. Impedimetric graphene-based biosensor for the detection of Escherichia coli DNA. Anal. Methods 6, 7935-7941 (2014
111. Heller I., et al. Identifying the Mechanism of Biosensing with Carbon Nanotube Transistors. Nano Lett. 8, 591-595 (2008
112. Heller I., et al. Influence of electrolyte composition on liquid-gated carbon nanotube, and graphene transistors. J. Am. Chem. Soc. 132, 17149-17156 (2010
113. Lin J., et al. Gating of single-layer graphene with single-stranded deoxyribonucleic acids. Small 6, 1150-1155 (2010
114. Dong X., Shi Y., Huang W., Chen P., & Li L.-J. Electrical detection of DNA hybridization with single-base specificity using transistors based on CVD-grown graphene sheets. Adv. Mater. 22, 1649-1653 (2010
115. Lu C., Yang H., Zhu C., Chen X., & Chen G. A graphene platform for sensing biomolecules. Angew. Chem. 121, 4879-4881 (2009
116. He S., et al. A graphene nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis. Adv. Funct. Mater. 20, 453-459 (2010
117. Balapanuru J., et al. A graphene oxide-organic dye ionic complex with DNA-sensing, and optical-limiting properties. Angew. Chem. 122, 6699-6703 (2010
118. Tao Y., Lin Y., Huang Z., Ren J., & Qu X. DNA-templated silver nanoclusters-graphene oxide nanohybrid materials: a platform for label-free, and sensitive fluorescence turn-on detection of multiple nucleic acid targets. Analyst 137, 2588-2592 (2012
119. Hu Y., Li F., Han D., & Niu L. Biocompatible Graphene for Bioanalytical Applications (Springer, 2014
120. Vicarelli L., Heerema S. J., Dekker C., & Zandbergen H. W. Controlling defects in graphene for optimizing the electrical properties of graphene nanodevices. ACS Nano 9, 3428-3435 (2015
121. Feng J., et al. Identification of single nucleotides in MoS2 nanopores. Nature Nanotech. 10, 1070-1076 (2015
122. Wei R., Martin T. G., Rant U., & Dietz H. DNA origami gatekeepers for solid-state nanopores. Angew. Chem. 124, 4948-4951 (2012
123. Bell N. A. W., et al. DNA origami nanopores. Nano Lett. 12, 512-517 (2012
124. Plesa C., et al. Ionic permeability, and mechanical properties of DNA origami nanoplates on solid-state nanopores. ACS Nano 8, 35-43 (2014
125. Jonsson M. P., & Dekker C. Plasmonic nanopore for electrical profiling of optical intensity landscapes. Nano Lett. 13, 1029-1033 (2013
126. Nam S., et al. Graphene nanopore with a self-integrated optical antenna. Nano Lett. 14, 5584-5589 (2014
127. Belkin M., Chao S.-H., Jonsson M. P., Dekker C., & Aksimentiev A. Plasmonic nanopores for trapping, controlling displacement, and sequencing of DNA. ACS Nano 9, 10598-10611 (2015
128. Chen Q., et al. 3D motion of DNA-Au nanoconjugates in graphene liquid cell electron microscopy. Nano Lett. 13, 4556-4561 (2013
129. Liu H., et al. Translocation of single-stranded DNA through single-walled carbon nanotubes. Science 327, 64-67 (2010
130. Siwy Z. S., & Davenport M. Making nanopores from nanotubes. Nature Nanotech. 5, 174-175 (2010