DNA-based optomechanical molecular motor

Journal of the American Chemical Society

Volumn 133, Issue 10, 2011, Pages 3452-3459

  McCullagh, Martin ^a   Franco, Ignacio ^a   Ratner, Mark A ^a   Schatz, George C ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFM; CANTILEVER STIFFNESS; CIS ISOMERS; DNA BASIS; DNA HAIRPIN; FREE-ENERGY CALCULATIONS; HAIRPIN STRUCTURES; MAXIMUM EFFICIENCY; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MOTORS; OPTOMECHANICAL; PHOTO-INDUCED; POTENTIALS OF MEAN FORCES; SINGLE-MOLECULE; STACKING INTERACTION; TRANS ISOMERS; WORK PER CYCLE;

ATOMIC FORCE MICROSCOPY; DNA; FREE ENERGY; HYDROGEN; HYDROGEN BONDS; MOLECULAR DYNAMICS; NUCLEIC ACIDS; PHOTOISOMERIZATION;

ISOMERS;

AZOBENZENE; DNA; MOLECULAR MOTOR; OPTOMECHANICAL MOLECULAR MOTOR; UNCLASSIFIED DRUG;

ARTICLE; ATOMIC FORCE MICROSCOPY; CALCULATION; CHEMICAL INTERACTION; DNA HAIRPIN; HYDROGEN BOND; ISOMER; ISOMERIZATION; MOLECULAR DYNAMICS; MOLECULAR SIZE;

DNA; ELASTICITY; ENTROPY; MECHANICAL PROCESSES; MICROSCOPY, ATOMIC FORCE; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION;

EID: 79952591094     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja109071a     Document Type: Article

References (50)

1. Ritort, F. J. Phys.: Condens. Matter 2006, 18, R531-R583
2. Evans, E. Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 105-128
3. Chen, F.; Tao, N. J. Acc. Chem. Res. 2009, 42, 429-438
4. Rief, M.; Oesterhelt, F.; Heymann, B.; Gaub, H. E. Science 1997, 275, 1295-1297
5. Liphardt, J.; Onoa, B.; Smith, S. B.; Tinoco, I.; Bustamante, C. Science 2001, 292, 733-737
6. Oberhauser, A. F.; Hansma, P. K.; Carrion-Vazquez, M.; Fernandez, J. M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 468-472
7. Jarzynski, C. Eur. Phys. J. B 2008, 64, 331-340
8. Park, S.; Schulten, K. J. Chem. Phys. 2004, 120, 5946-5961
9. Hummer, G.; Szabo, A. Acc. Chem. Res. 2005, 38, 504-513
10. Franco, I.; Schatz, G. C.; Ratner, M. A. J. Chem. Phys. 2009, 131, 124902
11. Balzani, V.; Credi, A.; Venturi, M. Molecular Devices and Machines-Concepts and Perspectives for the Nanoworld; Wiley-VCH: New York, 2008.
12. Hugel, T.; Holland, N. B.; Cattani, A.; Moroder, L.; Seitz, M.; Gaub, H. E. Science 2002, 296, 1103-1106
13. Holland, N. B.; Hugel, T.; Neuert, G.; Cattani-Scholz, A.; Renner, C.; Oesterhelt, D.; Moroder, L.; Seitz, M.; Gaub, H. E. Macromolecules 2003, 36, 2015-2023
14. Kumar, G. S.; Neckers, D. C. Chem. Rev. 1989, 89, 1915-1925
15. Griffith, J. Chem. Soc. Rev. 1972, 1, 481-493
16. Bortolus, P.; Monti, S. J. Phys. Chem. 1979, 83, 648-652
17. Dou, Y.; Hu, Y.; Yuan, S.; Wu, W.; Tang, H. Mol. Phys. 2009, 107, 181-190
18. Schaefer, L. V.; Mueller, M.; Gaub, H. E.; Grubmueller, H. Angew. Chem., Int. Ed. 2007, 46, 2232-2237
19. Shi, W.; Giannotti, M. I.; Zhang, X.; Hempenius, M. A.; Schönherr, H.; Vancso, G. J. Angew. Chem. 2007, 46, 8400-8404
20. Lehn, J. M. Supramolecular Chemistry: Concepts and Perspectives; Wiley-VCH: New York, 1995.
21. Collin, J.-P.; Gavina, P.; Heitz, V.; Sauvage, J.-P. Eur. J. Inorg. Chem. 1998, 1-14
22. Balzani, B. L.; Credi, A.; Raymo, F. M.; Stoddart, J. F. Angew. Chem., Int. Ed. 2000, 39, 3349
23. Feringa, B. L.; van Delden, R. A.; Koumura, N.; Geertsema, E. M. Chem. Rev. 2000, 100, 1789
24. Yang, Q.-Z.; Huang, Z.; Kucharski, T. J.; Khvostichenko, D.; Chen, J.; Boulatov, R. Nat. Nanotechnol. 2009, 4, 302-306
25. Creatini, L.; Cusati, T.; Granucci, G.; Persico, M. Chem. Phys. 2008, 347, 492-502
26. Neuert, G.; Hugel, T.; Netz, R. R.; Gaub, H. E. Macromolecules 2006, 39, 789-797
27. Asanuma, H.; Liang, X.; Yoshida, T.; Komiyama, M. Chem. Biol. Chem. 2001, 2, 39
28. Liang, X.; Asanuma, H.; Kashida, H.; Takasu, A.; Sakamoto, T.; Kawai, G.; Komiyama, M. J. Am. Chem. Soc. 2003, 125, 16408
29. Liu, M.; Asanuma, H.; Komiyama, M. J. Am. Chem. Soc. 2006, 128, 1009
30. Kang, H.; Liu, H.; Phillips, J. A.; Cao, Z.; Kim, Y.; Chen, Y.; Yang, Z.; Li, J.; Tan, W. Nano Lett. 2009, 9, 2690-2696
31. Tuma, J.; Tonzani, S.; Schatz, G. C.; Karaba, A. H.; Lewis, F. D. J. Phys. Chem. B 2007, 111, 13101-13106
32. Ferrenberg, A. M.; Swendsen, R. H. Phys. Rev. Lett. 1989, 63, 1195-1198
33. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021
34. Sarzynska, J.; Nilsson, L.; Kulinski, T. Biophys. J. 2003, 85, 3445-3459
35. Sorin, E. J.; Rhee, Y. M.; Pande, V. S. Biophys. J. 2005, 88, 2516-2524
36. Deng, N.-J.; Cieplak, P. Biophys. J. 2010, 98, 627-636
37. Santosh, M.; Maiti, P. K. J. Phys.: Condens. Matter 2009, 21, 034113
38. Case, D. A. AMBER 10; University of California: San Francisco, 2008.
39. Foloppe, N.; MacKerell, A. D. J. Comput. Chem. 2000, 21, 86-104
40. MacKerell, A. D.; Banavali, N. K. J. Comput. Chem. 2000, 21, 105-120
41. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97, 10269-10280
42. Brown, C. J. Acta Crystallogr. 1966, 21, 146
43. Mostad, A.; Romming, C. Acta Chem. Scand. 1971, 25, 3561-3568
44. Levine, B. G.; Martínez, T. J. Annu. Rev. Phys. Chem. 2007, 58, 613-634
45. Marsili, S.; Procacci, P. J. Phys. Chem. B 2010, 114, 2509 - 2516, PMID: 20121079.
46. Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. J. Comput. Phys. 1999, 151, 283-312
47. McCullagh, M.; Zhang, L.; Karaba, A. H.; Zhu, H.; Schatz, G. C.; Lewis, F. D. J. Phys. Chem. B 2008, 112, 11415-11421
48. Pohorille, A.; Ross, W. S.; Tinoco, J. I. Int. J. Supercomput. Appl. 1990, 4, 81-96
49. Krautbauer, R.; Rief, M.; Gaub, H. E. Nano Lett. 2003, 3, 493-496
50. Hagan, M. F.; Dinner, A. R.; Chandler, D.; Chakraborty, A. K. Proc. Natl. Acad. Sci. 2003, 100, 13922-13927