Computational studies of nucleotide selectivity in DNA-carbon nanotube hybrids

Journal of Physical Chemistry Letters

Volumn 3, Issue 19, 2012, Pages 2790-2797

  Mayo, Michael L ^a   Chen, Zheng Qian ^a   Kilina, Svetlana V ^a  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL STUDIES; FUNCTIONALIZED; INTERACTION MECHANISMS; INTERACTION STRENGTH; LATTICE VECTORS; MOLECULAR MECHANICALS; MORPHOLOGICAL PROPERTIES;

DNA SEQUENCES; GRAPHENE; MECHANICAL PROPERTIES; SINGLE-WALLED CARBON NANOTUBES (SWCN);

DNA;

EID: 84867148526     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz3011145     Document Type: Article

References (37)

1. Shi, J.; Cha, T.-G.; Claussen, J. C.; Diggs, A. R.; Choi, J. H.; Porterfield, D. M. Microbiosensors Based on DNA Modified Single-Walled Carbon Nanotube and Pt Black Nanocomposites Analyst 2011, 136, 4916-4924
2. Baker, J. R., Jr. Dendrimer-Based Nanoparticles for Cancer Therapy Hematology 2009, 2009, 708-719
3. Daniel, S.; Rao, T. P.; Rao, K. S.; Rani, S. U.; Naidu, G. R. K.; Lee, H.-T.; Kawai, T. A Review of DNA Functionalization/Grafted Carbon Nanotubes and their Characterization Sens. Actuators, B 2007, 122, 672-682
4. Vashist, S. K.; Zheng, D.; Pastorin, G.; Al-Rubeaan, K.; Luong, J. H.; Sheu, F.-S. Delivery of Drugs and Biomolecules Using Carbon Nanotubes Carbon 2011, 49, 4077-4097
5. Bhirde, A. A.; Patel, V.; Gavard, J.; Zhang, G.; Sousa, A. A.; Masedunskas, A.; Leapman, R. D.; Wiegert, R.; Gutkind, J. S.; Rusling, J. F. Targeted Killing of Cancer Cells In Vivo and In Vitro with EGF-Directed Carbon Nanotube-Based Drug Delivery ACS Nano 2009, 3, 307-316
6. Zhang, Y.; Bai, Y.; Yan, B. Functionalized Carbon Nanotubes for Potential Medicinal Applications Drug Discovery Today 2010, 115, 428-435
7. Pantarotto, D.; Singh, R.; McCarthy, D.; Erhardt, M.; Briand, J.-P.; Prato, M.; Kostarelos, K.; Bianco, A. Functionalized Carbon Nanotubes for Plasmid DNA Gene Delivery Angew. Chem. 2004, 116, 5354-5358
8. O'Connell, M. J.; Bachilo, S. M.; Huffman, C. B.; Moore, V. C.; Strano, M. S.; Haroz, E. H.; Rialon, K. L.; Boul, P. J.; Noon, W. H.; Kittrell, C. Band Gap Fluorescence From Individual Single-Walled Carbon Nanotubes Science 2002, 297, 593-596
9. Zheng, M.; Jagota, A.; Strano, M. S.; Santos, A. P.; Barone, P.; Chou, S. G.; Diner, B. A.; Dresselhaus, M. S.; Mclean, R. S.; Onoa, G. B. Structure-Based Carbon Nanotube Sorting by Sequence-Dependent DNA Assembly Science 2003, 302, 1545-1548
10. Tu, X.; Manohar, S.; Jagota, A.; Zheng, M. DNA Sequence Motifs for Structure-Specific Recognition and Separation of Carbon Nanotubes Nature 2009, 460, 250-253
11. Zhang, L.; Tu, X.; Welsher, K.; Wang, X.; Zheng, M.; Dai, H. DNA Encapsulation Inside Carbon Nanotubes Using Micro Electrolyte Plasmas J. Am. Chem. Soc. 2010, 131, 2454-2455
12. Gao, H.; Kong, Y. Simulation of DNA-Nanotube Interactions Annu. Rev. Mater. Res. 2004, 34, 123-150
13. Zhao, X.; Johnson, J. K. Simulation of Adsorption of DNA on Carbon Nanotubes J. Am. Chem. Soc. 2007, 129, 10438-10445
14. Johnson, R. R.; Johnson, A. T. C.; Klein, M. L. Probing the Structure of DNA-Carbon Nanotube Hybrids with Molecular Dynamics Nano Lett. 2008, 8, 69-75
15. Johnson, R. R.; Kohlmeyer, A.; Johnson, A. T. C.; Klein, M. L. Free Energy Landscape of a DNA-Carbon Nanotube Hybrid Using Replica Exchange Molecular Dynamics Nano Lett. 2009, 9, 537-541
16. Gao, H.; Kong, Y.; Cui, D. Spontaneous Insertion of DNA Oligonucleotides into Carbon Nanotubes Nano Lett. 2003, 3, 471-475
17. Kaneko, T.; Okada, T.; Hatakeyama, R. DNA Encapsulation Inside Carbon Nanotubes Using Micro Electrolyte Plasmas Contrib. Plasma Phys. 2007, 47, 57-63
18. Campbell, J. F.; Tessmer, I.; Thorp, H. H.; Erie, D. A. Atomic Force Microscopy Studies of DNA-Wrapped Carbon Nanotube Structure and Binding to Quantum Dots J. Am. Chem. Soc. 2008, 130, 10648-10655
19. Yarotski, D. A.; Kilina, S. V.; Talin, A. A.; Tretiak, S.; Prezhdo, O. V.; Balatsky, A. V.; Taylor, A. J. Scanning Tunneling Microscopy of DNA-Wrapped Carbon Nanotubes Nano Lett. 2009, 9, 12-17
20. Kilina, S.; Yarotski, D. A.; Talin, A. A.; Tretiak, S.; Taylor, A. J.; Balatsky, A. V. Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling J. Drug Delivery 2011, 2011, 1-9
21. Gigliotti, B.; Sakizzie, B.; Bethune, D.; Shelby, R.; Cha, J. Sequence-Independent Helical Wrapping of Single-Walled Carbon Nanotubes by Long Genomic DNA Nano Lett. 2006, 6, 159-164
22. Johnson, R. R.; Johnson, A. T. C.; Klein, M. L. The Nature of DNA-Base-Carbon-Nanotube Interactions Small 2010, 6, 31-34
23. Kilina, S.; Tretiak, S.; Doorn, S. K.; Luo, Z.; Papadimitrakopoulos, F.; Piryatinski, A.; Saxena, A.; Bishop, A. R. Cross-Polarized Excitons in Carbon Nanotubes Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6797-6802
24. Frey, J. T.;; Doren, D. J. TubeGen 3.4; University of Delaware: Newark, DE, 2011.
25. HyperChem Professional 7.5-8.0; Hypercube, Inc.: Gainesville, FL, 2007.
26. Foloppe, N.; MacKerell, A. D., Jr. All-Atom Empirical Force Field for Nucleic Acids: I. Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data J. Comput. Chem. 2000, 21, 86-104
27. MacKerell, A. D.; Banavali, N. K. All-Atom Empirical Force Field for Nucleic Acids: II. Application to Molecular Dynamics Simulations of DNA and RNA in Solution J. Comput. Chem. 2000, 21, 105-120
28. Hunter, C. A.; Sanders, J. K. M. The Nature of π-π Interactions J. Am. Chem. Soc. 1990, 112, 5525-5534
29. Husale, S.; Sahoo, S.; Radenovic, A.; Traversi, F.; Annibale, P.; Kis, A. ssDNA Binding Reveals the Atomic Structure of Graphene Langmuir 2010, 26, 18078-18082
30. Ahmed, T.; Kilina, S.; Das, T.; Haraldsen, J. T.; Balatsky, J. J. R. A. V. Electronic Fingerprints of DNA Bases on Graphene Nano Lett. 2012, 12, 927-931
31. Tanaka, H.; Kawai, T. Partial Sequencing of a Single DNA Molecule with a Scanning Tunneling Microscope Nat. Nanotechnol. 2009, 4, 518-522
32. 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
33. McGaughey, G. B.; Gagné, M.; Rappé, A. K. π-Stacking Interactions: ALIVE AND WELL IN PROTIENS J. Biol. Chem. 1998, 273, 15458-15463
34. Humphrey, W.; Dalke, A.; Schulten, K. VMD -Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
35. Varghese, N.; Mogera, U.; Govindaraj, A.; Das, A.; Maiti, P. K.; Sood, A. K.; Rao, C. N. R. Binding of DNA Nucleobases and Nucleosides with Graphene ChemPhysChem 2009, 10, 206-210
36. Sowerby, S. J.; Cohn, C. A.; Heckl, W. M.; Holm, N. G. Differential Adsorption of Nucleic Acid Bases: Relevance to the Origin of Life Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 820-822
37. Antony, J.; Grimme, S. Structures and Interaction Energies of Stacked Graphene-Nucleobase Complexes Phys. Chem. Chem. Phys. 2008, 10, 2722-2729