Electronic excitations and spectra in single-stranded DNA

Journal of the American Chemical Society

Volumn 130, Issue 24, 2008, Pages 7607-7612

  Tonzani, Stefano ^a   Schatz, George C ^a  

^a NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; DNA; GENES; MECHANICS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULES; NUCLEIC ACIDS; ORGANIC ACIDS; PROBABILITY DENSITY FUNCTION; QUANTUM CHEMISTRY;

DELOCALIZATION; DELOCALIZED STATES; DENSITY-FUNCTIONAL (DF); DOUBLE-STRANDED DNA (DS-DNA); ELECTRONIC EXCITATIONS (EE); EXPERIMENTAL RESULTS; MOLECULAR DYNAMICS CALCULATIONS; MOLECULAR DYNAMICS SIMULATIONS (MDS); POLY(A); SINGLE STRANDED DNA (SS DNA); SPECTRA (CO);

DYNAMICS;

DOUBLE STRANDED DNA; SINGLE STRANDED DNA;

ARTICLE; CALCULATION; CIRCULAR DICHROISM; DENSITY FUNCTIONAL THEORY; DNA STRUCTURE; ELECTROSTIMULATION; MOLECULAR DYNAMICS; SIMULATION; VALIDATION STUDY;

ADENOSINE; CIRCULAR DICHROISM; DNA, SINGLE-STRANDED; ELECTRONS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; POLYDEOXYRIBONUCLEOTIDES;

EID: 45249104625     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja7103894     Document Type: Article

References (44)

1. Tinoco, I., Jr J. Am. Chem. Soc. 1960, 82, 4785.
2. Cadet, J.; Sageb, E.; Douki, T. Mutat. Res. 2005, 571, 3.
3. Tuma, J.; Tonzani, S.; Schatz, G. C.; Karaba, A. H.; Lewis, F. D. J. Phys. Chem. B 2007, 111, 13101.
4. Eisinger, J.; Shulman, R. G. Science 1968, 161, 1311.
5. Eisinger, J.; Gueron, M.; Shulman, R. G.; Yamane, T. Proc. Natl. Acad. Sci. U.S.A. 1966, 55, 1015.
6. Crespo-Hernandez, C. E.; Cohen, B.; Kohler, B. Nature 2005, 436, 1141.
7. Bouvier, B.; Dognon, J.-P.; Lavery, R.; Markovitsi, D.; Millie, P.; Onidas, D.; Zakrzewska, K. J. Phys. Chem. B 2003, 107, 13512.
8. Buchvarov, I.; Wang, Q.; Raytchev, M.; Trifonov, A.; Fiebig, T. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4794.
9. Schultz, T.; Samoylova, E.; Radloff, W.; Hertel, I. V.; Sobolewski, A. L.; Domcke, W. Science 2004, 306, 1765.
10. Olsthoorn, C. S. M.; Bostelaar, L. J.; De Rooij, J. F. M.; Van Boom, J. H.; Altona, C. Eur. J. Biochem. 1981, 115, 309.
11. Zimmer, C.; Birch-Hirschfeld, E.; Weiss, R. Nucleic Acids Res. 1974, 1, 1017.
12. Greve, J.; Mestre, N. F.; Levin, A. Biopolymers 1977, 16, 1489.
13. Cheatham, T. E., III; Kollman, P. A. Annu. Rev. Phys. Chem. 2000, 51, 435.
14. Martinez, J. M.; Elmroth, S. K. C.; Kloo, L. J. Am. Chem. Soc. 2001, 123, 12279.
15. Sen, S.; Nilsson, L. J. Am. Chem. Soc. 2001, 123, 7414.
16. Kohli, P.; Harrell, C. C.; Cao, Z.; Gasparac, R.; Tan, W.; Martin, C. R. Science 2004, 305, 984.
17. Seeman, N. C. Nature 2003, 421, 427.
18. Stokes, G. Y.; Gibbs-Davis, J. M.; Boman, F. C.; Stepp, B. R.; Condie, A. G.; Nguyen, S. T.; Geiger, F. M. J. Am. Chem. Soc. 2007, 129, 7492.
19. Gerland, U.; Bundschuh, R.; Hwa, T. Phys. Biol. 2004, 1, 19.
20. Ruvkun, G. Science 2001, 294, 797.
21. Kim, Y. T.; Tabor, S.; Bortner, C.; Griffith, J. D.; Richardson, C. C. J. Biol. Chem. 1992, 267, 15022.
22. Summers, M. F. J. Cell. Biochem. 1991, 45, 41.
23. Thomas, J. L.; Tobias, D. J.; MacKerell, A. D., Jr J. Phys. Chem. B 2007, 111, 12941.
24. Grozema, F. C.; Tonzani, S.; Berlin, Y. B.; Schatz, G. C.; Siebbeles, L. D. A.; Ratner, M. A. J. Am. Chem. Soc. 2008, 130, 5157.
25. Wang, J.; Cieplak, P.; Kollman, P. A. J. Comput. Chem. 2000, 21, 1049.
26. te Velde, G.; Bickelhaupt, F. M.; Baerends, E. J.; Guerra, C. F.; van Gisbergen, S. J. A.; Snijders, J. G.; Ziegler, T. J. Comput. Chem. 2001, 22, 931967.
27. Autschbach, J.; Ziegler, T.; van Gisbergen, S. J. A.; Baerends, E. J. J. Chem. Phys. 2002, 116, 6930.
28. Gritsenko, O. V.; Schipper, P. R. T.; Baerends, E. J. Chem. Phys. Lett. 1999, 302, 199.
29. Patchkovskii, S.; Autschbach, J.; Ziegler, T. J. Chem. Phys. 1999, 115, 26.
30. Isaksson, J.; Acharya, S.; Barman, J.; Cheruku, P.; Chattopadhyaya, J. Biochemistry 2004, 43, 15996.
31. Goddard, N. L.; Bonnet, G.; Krichevsky, O.; Libchaber, A. Phys. Rev. Lett. 2000, 85, 2400.
32. Stellwagen, E.; Abdulla, A.; Qian, D.; Stellwagen, N. C. Biochemistry 2007, 46, 10931.
33. Dixit, S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E.; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Biophys. J. 2005, 89, 3721.
34. Tinland, B.; Pluen, A.; Sturm, J.; Weill, G. Macromolecules 1997, 30, 5763.
35. Hu, L. H.; Zhao, Y.; Wang, F.; Chen, G. H.; Ma, C.: Kwok, W.-M.; Phillips, D. L. J. Phys. Chem. B 2007, 111, 11812.
36. Lewis, J. P.; Cheatham, T. E.; Starikov, E. B.; Wang, H.; Sankey, O. F. J. Phys. Chem. B 2003, 107, 2581.
37. Mantz, Y. A.; Gervasio, F. L.; Laino, T.; Parrinello, M. Phys. Rev. Lett. 2007, 99, 058104.
38. Conwell, E. M. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 8795.
39. Kurnikov, I. V.; Tong, G. S. M.; Madrid, M.; Beratan, D. N. J. Phys. Chem. B 2002, 106, 7.
40. Conwell, E. N.; McLaughlin, P. M.; Bloch, S. M. J. Phys. Chem. B 2008, 112, 2268.
41. Hudock, H. R.; Levine, B. G.; Thompson, A. L.; Satzger, H.; Townsend, D.; Gador, N.; Ullrich, S.; Stolow, A.; Martinez, T. J. J. Phys. Chem. A 2007, 111, 8500.
42. Craig, C. F.; Duncan, W. R.; Prezhdo, O. V. Phys. Rev. Lett. 2005, 95, 163001.
43. Maitra, N. T. J. Chem. Phys. 2006, 125, 014110.
44. Santoro, F.; Barone, V.; Improta, R. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9931.