Groove binding mechanism of ionic liquids: A key factor in long-term stability of DNA in hydrated ionic liquids?

Journal of the American Chemical Society

Volumn 134, Issue 50, 2012, Pages 20330-20339

  Chandran, Aneesh ^a   Ghoshdastidar, Debostuti ^a   Senapati, Sanjib ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY MADRAS   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING CHARACTERISTICS; DISPLACEMENT ASSAY; DNA STABILITY; ELECTROSTATIC ASSOCIATION; FLUORESCENT DYES; FORENSIC SCIENCE; GROOVE BINDING; HYDROLYTIC REACTIONS; KEY FACTORS; LONG TERM STABILITY; MINOR GROOVES; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANISM; POLAR INTERACTIONS; SAMPLE STORAGE; SPECTRAL MEASUREMENT; WATER CAGE;

ASSOCIATION REACTIONS; HYDRATION; IONIC LIQUIDS; MOLECULAR DYNAMICS; POSITIVE IONS;

DNA;

CATION; DNA; FLUORESCENT DYE; HYDRATED IONIC LIQUID; IONIC LIQUID; UNCLASSIFIED DRUG;

ABSORPTION SPECTROSCOPY; ARTICLE; CIRCULAR DICHROISM; CONTROLLED STUDY; DNA BINDING; DNA CONFORMATION; DNA DENATURATION; HYDRATION; HYDROLYSIS; HYDROPHOBICITY; MOLECULAR DYNAMICS; PROTEIN INTERACTION; PROTEIN STABILITY; SOLVATION; STATIC ELECTRICITY; ULTRAVIOLET SPECTROSCOPY;

CIRCULAR DICHROISM; DNA; FLUORESCENT DYES; IONIC LIQUIDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; THERMODYNAMICS;

EID: 84871398589     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja304519d     Document Type: Article

References (45)

1. Kutzler, M. A.; Weiner, D. B. Nat. Rev. Genet. 2008, 9, 776-788
2. Jobling, M. A.; Gill, P. Nat. Rev. Genet. 2004, 5, 739-751
3. Krishnan, Y.; Simmel, F. C. Angew. Chem., Int. Ed. 2011, 50, 3124-3156
4. Lukin, M.; de los Santos, C. Chem. Rev. 2006, 106, 607-686
5. Roder, B.; Fruhwirth, K.; Vogl, C.; Wagner, M.; Rossmanith, P. J. Clin. Microbiol. 2010, 48, 4260-4262
6. Bonnet, J.; Colotte, M.; Coudy, D.; Couallier, V.; Portier, J.; Morin, B.; Tuffet, S. Nucleic Acids Res. 2010, 38, 1531-1546
7. Kokorin, A., Ed. Ionic Liquids: Applications and Perspectives; InTech: Rijeka, Croatia, 2011.
8. Qin, W.; Li, S. F. Y. Analyst 2003, 128, 37-41
9. Nishimura, N.; Nomura, Y.; Nakamura, N.; Ohno, H. Biomaterials 2005, 26, 5558-5563
10. Wang, J. H.; Cheng, D. H.; Chen, X. W.; Du, Z.; Fang, Z. L. Anal. Chem. 2007, 79, 620-625
11. de Zoysa, R. S. S.; Jayawardhana, D. A.; Zhao, Q.; Wang, D.; Armstrong, D. W.; Guan, X. J. Phys. Chem. B 2009, 113, 13332-13336
12. Vijayaraghavan, R.; Izgorodin, A.; Ganesh, V.; Surianarayanan, M.; MacFarlane, D. R. Angew. Chem., Int. Ed. 2010, 49, 1631-1633
13. Ding, Y.; Zhang, L.; Xie, J.; Guo, R. J. Phys. Chem. B 2010, 114, 2033-2043
14. Paul, A.; Mandal, P. K.; Samanta, A. J. Phys. Chem. B 2005, 109, 9148-9153
15. Perez, A.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 2007, 129, 14739-14745
16. Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E., III; Laughton, C. A.; Orozco, M. Biophys. J. 2007, 92, 3817-3829
17. Lopes, J. N. C.; Padua, A. A. H. J. Phys. Chem. B 2006, 110, 19586-19592
18. Sambasivarao, S. V.; Acevedo, O. J. Chem. Theory Comput. 2009, 5, 1038-1050
19. Case, D. A.; AMBER 11; University of California: San Francisco, 2010.
20. El Hassan, M. A.; Calladine, C. R. J. Mol. Biol. 1998, 282, 331-343
21. Altona, C.; Sundaralingam, M. J. Am. Chem. Soc. 1972, 94 (23) 8205-8212
22. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Acc. Chem. Res. 2000, 33, 889-897
23. Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. J. Am. Chem. Soc. 2000, 123, 5221-5230
24. Mascarenhas, N. M.; Kastner, J. BMC Struct. Biol. 2012, 12, 8
25. Huang, M.-M.; Jiang, J.; Sasisanker, P.; Driver, G. W.; Weingartner, H. J. Chem. Eng. Data 2011, 56, 1494-1499
26. 3], 44; [choline][lactate], 69.
27. Treesuwan, W.; Wittayanarakul, K.; Anthony, N. G.; Huchet, G.; Alniss, H.; Hannongbua, S.; Khalaf, A. I.; Suckling, C. J.; Parkinson, J. A.; Mackay, S. P. Phys. Chem. Chem. Phys. 2009, 11, 10682-10693
28. Boger, D. L.; Fink, B. E.; Brunette, S. R.; Tse, W. C.; Hedrick, M. P. J. Am. Chem. Soc. 2001, 123, 5878-589
29. 2/s.
30. Cardoso, L.; Micaelo, N. M. ChemPhysChem 2011, 12, 275-277
31. Wang, H.; Wang, J.; Zhang, S. Phys. Chem. Chem. Phys. 2011, 13, 3906-3910
32. Xie, Y. N.; Wang, S. F.; Zhang, Z. L.; Pang, D. W. J. Phys. Chem. B 2008, 112, 9864-9868
33. Neidle, S. Nat. Prod. Rep. 2001, 18, 291-309
34. Dolenc, J.; Oostenbrink, C.; Koller, J.; van Gunsteren, W. F. Nucleic Acids Res. 2005, 33, 725-733
35. Schneider, B.; Patel, K.; Berman, H. M. Biophys. J. 1998, 75, 2422-2434
36. Fujita, K.; MacFarlane, D. R.; Forsyth, M. Chem. Commun. 2005, 4804-4806
37. Fujita, K.; MacFarlane, D. R.; Forsyth, M.; Fujita, M. Y.; Murata, K.; Nakamura, N.; Ohno, H. Biomacromolecules 2007, 8, 2080-2086
38. Drew, H. R.; Dickerson, R. E. J. Mol. Biol. 1981, 151, 535-556
39. Arai, S.; Chatake, T.; Ohhara, T.; Kurihara, K.; Tanaka, I.; Suzuki, N.; Fujimoto, Z.; Mizuno, H.; Niimura, N. Nucleic Acids Res. 2005, 33, 3017-3024
40. Subramanian, P. S.; Ravishanker, G.; Beveridge, D. L. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 1836-1840
41. Chalikian, T. V.; Eric Plum, G.; Sarvazyan, A. P.; Breslauer, K. J. Biochemistry 1994, 33, 8629-8640
42. Jordan, C. F.; Lerman, L. S.; Venable, J. H., Jr. Nat. New Biol. 1972, 236, 67-70
43. Parodi, S.; Kendall, F.; Nicolini, C. Nucleic Acids Res. 1975, 2, 477-486
44. Sinha, R.; Islam, M. M.; Bhadra, K.; Kumar, G. S.; Banerjee, A.; Maiti, M. Bioorg. Med. Chem. 2006, 14, 800-814
45. Lavelle, N.; Lee, S. A.; Flox, L. S. Phys. Rev. 1991, 43, 3126-3130