Two dimensional molecular electronics spectroscopy for molecular fingerprinting, DNA sequencing, and cancerous dna recognition

ACS Nano

Volumn 8, Issue 2, 2014, Pages 1827-1833

  Rajan, Arunkumar Chitteth ^a   Rezapour, Mohammad Reza ^a   Yun, Jeonghun ^a   Cho, Yeonchoo ^a   Cho, Woo Jong ^a   Min, Seung Kyu ^a   Lee, Geunsik ^a   Kim, Kwang S ^a,b  

^a Pohang University of Science and Technology (POSTECH)   (South Korea)

^b Ulsan National Institute of Science and Technology   (South Korea)

Author keywords

DNA sequencing; electron transport; Fano resonance; methylated DNA; molecular electronics spectroscopy

Indexed keywords

DNA;

ARTICLE; CHEMISTRY; DNA SEQUENCE; METABOLISM; METHODOLOGY; SPECTROSCOPY;

DNA, NEOPLASM; SEQUENCE ANALYSIS, DNA; SPECTRUM ANALYSIS;

EID: 84894638908     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn4062148     Document Type: Article

References (50)

1. Ratner, M. A Brief History of Molecular Electronics Nat. Nanotechnol. 2013, 8, 378-381
2. Song, H.; Kim, Y.; Jang, H.-W.; Jeong, H.; Reed, M. A.; Lee, T. Observation of Molecular Orbital Gating Nature 2009, 462, 1039-1043
3. Cuniberti, G.; Fagas, G.; Richter, K. Introducing Molecular Electronics; Springer: New York, 2005.
4. Kim, W. Y.; Choi, Y. C.; Min, S. K.; Cho, Y.; Kim, K. S. Application of Quantum Chemistry to Nanotechnology: Electron and Spin Transport in Molecular Devices Chem. Soc. Rev. 2009, 38, 2319-2333
5. Cho, W. J.; Cho, Y.; Min, S. K.; Kim, W. Y.; Kim, K. S. Chromium Porphyrin Arrays as Spintronic Devices J. Am. Chem. Soc. 2011, 133, 9364-9369
6. Shen, L.; Zeng, M.; Yang, S. W.; Zhang, C.; Wang, X.; Feng, Y. Electron Transport Properties of Atomic Carbon Nanowires Between Graphene Electrodes J. Am. Chem. Soc. 2010, 132, 11481-11486
7. Shendure, J.; Ji, H. Next-Generation DNA Sequencing Nat. Biotechnol. 2008, 26, 1135-1145
8. Huang, S.; He, J.; Chang, S.; Zhang, P.; Liang, F.; Li, S.; Tuchband, M.; Fuhrmann, A.; Ros, R.; Lindsay, S. Identifying Single Bases in a DNA Oligomer with Electron Tunnelling Nat. Nanotechnol. 2010, 5, 868-873
9. Tsutsui, M.; Taniguchi, M.; Yokota, K.; Kawai, T. Identifying Single Nucleotides by Tunnelling Current Nat. Nanotechnol. 2010, 5, 286-290
10. 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. 2011, 11, 1941-1945
11. Scheicher, R. H.; Grigoriev, A.; Ahuja, R. DNA Sequencing with Nanopores from an ab Initio Perspective J. Mater. Sci. 2012, 47, 7439-7446
12. Ahmed, T.; Kilina, S.; Das, T.; Haraldsen, J. T.; Rehr, J. J.; Balatsky, A. V. Electronic Fingerprints of DNA Bases on Graphene Nano Lett. 2012, 12, 927-931
13. Nelson, T.; Zhang, B.; Prezhdo, O. V. Detection of Nucleic Acids with Graphene Nanopores: Ab Initio Characterization of a Novel Sequencing Device Nano Lett. 2010, 10, 3237-3242
14. 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. 2012, 12, 50-55
15. Zwolak, M.; Di Ventra, M. Colloquium: Physical Approaches to DNA Sequencing and Detection Rev. Mod. Phys. 2008, 80, 141-165
16. Lagerqvist, J.; Zwolak, M.; Di Ventra, M. Fast DNA Sequencing via Transverse Electronic Transport Nano Lett. 2006, 6, 779-782
17. Min, S. K.; Kim, W. Y.; Cho, Y.; Kim, K. S. Fast DNA Sequencing with a Graphene Based Nanochannel Device Nat. Nanotechnol. 2011, 6, 162-165
18. Jaenisch, R.; Bird, A. Epigenetic Regulation of Gene Expression: How the Genome Integrates Intrinsic and Environmental Signals Nat. Genet. 2003, 33, 245-254
19. Clark, S. J.; Statham, A.; Stirzaker, C.; Molloy, P. L.; Frommer, M. DNA Methylation: Bisulphite Modification and Analysis Nat. Protoc. 2006, 1, 2353-2364
20. Fano, U. Effects of Configuration Interaction on Intensities and Phase Shifts Phys. Rev. 1961, 124, 1866-1878
21. Miroshnichenko, A. E.; Flach, S.; Kivshar, Y. S. Fano Resonances in Nanoscale Structures Rev. Mod. Phys. 2010, 82, 2257-2298
22. Fan, S.; Suh, W.; Joannopoulos, J. D. Temporal Coupled-Mode Theory for the Fano Resonance in Optical Resonators J. Opt. Soc. Am. A 2003, 20, 569-572
23. Kim, J.; Kim, J.-R.; Lee, J.-O.; Park, J. W.; So, H. M.; Kim, N.; Kang, K.; Yoo, K.-H.; Kim, J.-J. Fano Resonance in Crossed Carbon Nanotubes Phys. Rev. Lett. 2003, 90, 166403
24. Miroshnichenko, A. E.; Mingaleev, S. F.; Flach, S.; Kivshar, Y. S. Nonlinear Fano Resonance and Bistable Wave Transmission Phys. Rev. E 2005, 71, 036626
25. Sasaki, S.; Tamura, H.; Akazaki, T.; Fujisawa, T. Fano-Kondo Interplay in a Side Coupled Double Quantum Dot Phys. Rev. Lett. 2009, 103, 266806
26. K. S. Novoselov, K. S.; Geim, A. K.; Morozov, S. V.; Jiang, D.; Zhang, Y.; Dubonos, S. V.; Grigorieva, I. V.; Firsov, A. A. Electric Field Effect in Atomically Thin Carbon Film Science 2004, 306, 666-669
27. Kim, K. S.; Zhao, Y.; Jang, H.; Lee, S. Y.; Kim, J. M.; Kim, K. S.; Ahn, J.-H.; Kim, P.; Choi, J.-Y.; Hong, B. H. Large-Scale Pattern Growth of Graphene Films for Stretchable Transparent Electrodes Nature 2009, 457, 706-710
28. Son, Y.-W.; Cohen, M. L.; Louie, S. G. Half-Metallic Graphene Nanoribbons Nature 2006, 444, 347-349
29. Kim, W. Y.; Kim, K. S. Prediction of Very Large Values of Magnetoresistance in a Graphene Nanoribbon Device Nat. Nanotechnol. 2008, 3, 408-412
30. Tworzydło, J.; Trauzettel, B.; Titov, M.; Rycerz, A.; Beenakker, C. W. J. Sub-Poissonian Shot Noise in Graphene Phys. Rev. Lett. 2006, 96, 246802
31. Cai, J.; Ruffieux, P.; Jaafar, R.; Bieri, M.; Braun, T.; Blankenburg, S.; Muoth, M.; Seitsonen, A. P.; Saleh, M.; Feng, X. et al. Atomically Precise Bottom-Up Fabrication of Graphene Nanoribbons Nature 2010, 466, 470-473
32. Chen, Y.-C.; Oteyza, D. G. d.; Pedramrazi, Z.; Chen, C.; Fischer, F. R.; Crommie, M. F. Tuning the Band Gap of Graphene Nanoribbons Synthesized from Molecular Precursors ACS Nano 2013, 7, 6123-6128
33. Koch, M.; Ample, F.; Joachim, C.; Grill, L. Voltage-Dependent Conductance of a Single Graphene Nanoribbon Nat. Nanotechnol. 2012, 7, 713-717
34. Kim, K. S.; Tarakeshwar, P.; Lee, J. Y. Molecular Clusters of π-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies Chem. Rev. 2000, 100, 4145-4186
35. Georgakilas, V.; Otyepka, M.; Bourlinos, A. B.; Chandra, V.; Kim, N.; Kemp, K. C.; Hobza, P.; Zboril, R.; Kim, K. S. Functionalization of Graphene: Covalent and Non-covalent Approaches, Derivatives and Applications Chem. Rev. 2012, 112, 6156-6214
36. 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. 2011, 13, 14293-14296
37. Kim, W. Y.; Kim, K. S. Tuning Molecular Orbitals in Molecular Electronics and Spintronics Acc. Chem. Res. 2010, 43, 111-120
38. Meng, S.; Maragakis, P.; Papaloukas, C.; Kaxiras, E. DNA Nucleoside Interaction and Identification with Carbon Nanotubes Nano Lett. 2007, 7, 45-50
39. Cho, Y.; Min, S. K.; Yun, J.; Kim, W. Y.; Tkatchenko, A.; Kim, K. S. Noncovalent Interactions of DNA Bases with Naphthalene and Graphene J. Chem. Theory Comput. 2013, 9, 2090-2096
40. 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 2013, 117, 13435-13441
41. Haskins, J.; KInacI, A.; Sevik, C.; Sevinçli, H.; Cuniberti, G.; Çag̀In, T. Control of Thermal and Electronic Transport in Defect-Engineered Graphene Nanoribbons ACS Nano 2011, 5, 3779-3787
42. Diefenbach, M.; Kim, K. S. Towards Molecular Magnetic Switching with an Electric Bias Angew. Chem., Int. Ed. 2007, 46, 7640-7643
43. Datta, S. Electronic Transport in Mesoscopic Systems; Cambridge University Press: Cambridge, 1997.
44. Brandbyge, M.; Mozos, J.-L.; Ordejón, P.; Taylor, J.; Stokbro, K. Density-Functional Method for Nonequilibrium Electron Transport Phys. Rev. B 2002, 65, 165401
45. Taylor, J.; Guo, H.; Wang, J. Ab Initio Modeling of Quantum Transport Properties of Molecular Electronic Devices Phys. Rev. B 2001, 63, 245407
46. Perdew, J. P.; Zunger, A. Self-Interaction Correction to Density-Functional Approximations for Many-Electron Systems Phys. Rev. B. 1981, 23, 5048
47. Troullier, N.; Martins, J. L. Efficient Pseudopotentials for Plane-Wave Calculations Phys. Rev. B 1991, 43, 1993-2006
48. Kim, W. Y.; Kim, K. S. Carbon Nanotube, Graphene, Nanowire, and Molecule-Based Electron and Spin Transport Phenomena Using the Nonequilibrium Green's Function Method at the Level of First Principles Theory J. Comput. Chem. 2008, 29, 1073-1083
49. Soler, J. M.; Artacho, E.; Gale, J. D.; García, A.; Junquera, J.; Ordejón, P.; Sánchez-Portal, D. The SIESTA Method for ab Initio Order-N Materials Simulation J. Phys.: Condens. Matter 2002, 14, 2745-2779
50. Lee, D. H.; Joannopoulos, J. D. Simple Scheme for Surface-Band Calculations. I Phys. Rev. B 1981, 23, 4988-4996