Conformation dependence of DNA exciton parentage

Journal of Physical Chemistry B

Volumn 113, Issue 30, 2009, Pages 10428-10435

  Starikov, E B ^a,b   Cuniberti, G ^a,b   Tanaka, Shigenori ^c  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

^c KOBE UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DNA; EXCITONS; GENES; NUCLEIC ACIDS;

COMPUTATIONAL RESULTS; DNA DUPLEXES; ELECTRONIC EXCITATION; ELECTRONIC TRANSITION; INTERMEDIATE NEGLECT OF DIFFERENTIAL OVERLAP; MANY-ELECTRON TRANSITIONS; OSCILLATOR STRENGTHS; SEMI-EMPIRICAL; SINGLE ELECTRON; TETRAMERS;

DNA SEQUENCES;

EID: 67651211710     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9035869     Document Type: Article

References (46)

1. Crespo-Hernandez, C. E.; Cohen, B.; Hare, P. M.; Kohler, B. Ultrafast excited-state dynamics in nucleic acids. Chem. Rev. 2004, 104, 1977-2019.
2. Markovitsi, D.; Gustavsson, T.; Talbot, F. Excited states and energy transfer among DNA bases in double helices. Photochem. Photobiol. Sci. 2007, 6, 717-724.
3. Schwalb, N.; Temps, F. Base Sequence and Higher-Order Structure Induce the Complex Excited-State Dynamics in DNA. Science 2008, 322, 243-245.
4. Takaya, T.; Su, C.; de la Harpe, K.; Crespo-Hernandez, C. E.; Kohler, B. UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 10285-10290.
5. Buchvarov, I.; Wang, Q.; Raytchev, M.; Trifonov, A.; Fiebig, T. Electronic energy delocalization and dissipation in single- and double-stranded DNA. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4794-4797.
6. Markovitsi, D.; Talbot, F.; Gustavsson, T.; Onidas, D.; Lazzarotto, E.; Marguet, S. Molecular spectroscopy: Complexity of excited-state dynamics in DNA. Nature 2006, 441, E7.
7. Crespo-Hernandez, C. E.; Cohen, B.; Kohler, B. Molecular spectroscopy: Complexity of excited-state dynamics in DNA (reply). Nature 2006, 441, E8.
8. Warshaw, M. M.; Tinoco, I., Jr. Optical properties of sixteen dinucleoside phosphates. J. Mol. Biol. 1966, 20, 29-38.
9. Georghiou, S.; Thomas, D.; Bradrick, T. D.; Philippetis, A.; Beechem, J. M. Large-Amplitude Picosecond Anisotropy Decay of the Intrinsic Fluorescence of Double-Stranded DNA. Biophys. J. 1996, 70, 1909-1922.
10. Georghiou, S.; Kubala, S. M.; Catherine, C.; Large, C. C. Environmental Control of the Deformability of the DNA Double Helix. Photochem. Photobiol. 1998, 67, 526-531.
11. Czader, A.; Bittner, E. R. Calculations of the exciton coupling elements between the DNA bases using the transition density cube method. J. Chem. Phys. 2008, 128, 035101.
12. Voityuk, A. A.; Roesch, N.; Bixon, M.; Jortner, J. Electronic Coupling for Charge Transfer and Transport in DNA. J. Phys. Chem. B 2000, 104, 9740-9745.
13. Voityuk, A. A.; Bixon, M.; Jortner, J.; Roesch, N. Electronic coupling between Watson-Crick pairs for hole transfer and transport in desoxyribonucleic acid. J. Chem. Phys. 2001, 114, 5614-5620.
14. Mehrez, H.; Anantram, M. P. Interbase electronic coupling for transport through DNA. Phys. Rev. B 2005, 71, 115405.
15. Yanson, I. K.; Teplitsky, A. B.; Sukhodub, L. F. Experimental studies of molecular interactions between nitrogen bases of nucleic acids. Biopolymers 1979, 18, 1149-1170.
16. Starikov, E. B. Quantum chemistry of nucleic acids: how it could help and when it is necessary. J. Photochem. Photobiol., C 2002, 3, 147-164.
17. Starikov, E. B. Mechanisms of charge carrier generation in polycrystalline DNA fibers. Phys. Chem. Chem. Phys. 2002, 4, 4523-4527.
18. Starikov, E. B. Role of electron correlations in deoxyribonucleic acid duplexes: is an extended Hubbard Hamiltonian a good model in this case Philos. Mag. Lett. 2003, 83, 699-708.
19. Starikov, E. B. Importance of Charge Transfer Excitation in DNA Electron Spectrum: A ZINDO Semiempirical Quantum-Chemical Study. Mod. Phys. Lett. B 2004, 18, 825-831.
20. Starikov, E. B.; Lewis, J. P.; Sankey, O. Base sequence effects on charge carrier generation in DNA: A theoretical study. Int. J. Mod. Phys. B 2005, 19, 4331-4557.
21. Conwell, E. M.; McLaughlin, P. M.; Bloch, S. M. Charge-Transfer Excitons in DNA. J. Phys. Chem. B 2008, 112, 2268-2272.
22. Burin, A. L.; Dickman, J. A.; Uskov, D. B.; Hebbard, C. F. F.; Schatz, G. C. Optical absorption spectra and monomer interaction in polymers: Investigation of exciton coupling in DNA hairpins. J. Chem. Phys. 2008, 129, 091102.
23. Sobolewski, A. L.; Domcke, W.; Hättig, C. Tautomeric selectivity of the excited-state lifetime of guanine cytosine base pairs: The role of electron-driven proton-transfer processes. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17903-17906.
24. Groenhof, G.; Schäfer, L. V.; Boggio-Pasqua, M.; Goette, M.; Grubmüller, H.; Robb, M. A. Ultrafast Deactivation of an Excited Cytosine-Guanine Base Pair in DNA. J. Am. Chem. Soc. 2007, 129, 6812-6819.
25. Schwalb, N. K.; Temps, F. Ultrafast Electronic Relaxation in Guanosine is Promoted by Hydrogen Bonding with Cytidine. J. Am. Chem. Soc. 2007, 129, 9272-9273.
26. Miannay, F. A.; Banyasz, A.; Gustavsson, T.; Markovitsi, D. Ultrafast Excited-State Deactivation and Energy Transfer in Guanine-Cytosine DNA Double Helices. J. Am. Chem. Soc. 2007, 129, 14574-14575.
27. Voityuk, A. A. Assessment of semiempirical methods for the computation of charge transfer in DNA pi-stacks. Chem. Phys. Lett. 2006, 427, 177-180.
28. Voityuk, A. A. Electronic couplings and on-site energies for hole transfer in DNA: Systematic quantum mechanical/molecular dynamic study. J. Chem. Phys. 2008, 128, 115101.
29. Siriwong, K.; Voityuk, A. A. Pi-stack structure and hole transfer in DNA hairpins and DNA. A combined QM/MD study. J. Phys. Chem. B 2008, 112, 8181-8187.
30. Reha, D.; Barford, W.; Harris, S. A multi-scale method for the calculation of charge transfer rates through the Pi-stack of DNA: application to DNA dynamics. Phys. Chem. Chem. Phys. 2008, 10, 5436-5444.
31. Hutchison, G. R.; Ratner, M. A.; Marks, T. J. Accurate prediction of band gaps in neutral heterocyclic conjugated polymers. J. Phys. Chem. A 2002, 106, 10596-10605.
32. Varsano, D.; Di Felice, R.; Marques, M. A. L.; Rubio, A. A TDDFT study of the excited states of DNA bases and their assemblies. J. Phys. Chem. B 2006, 110, 7129-7138.
33. Santoro, F.; Barone, V.; Improta, R. Influence of base stacking on excited-state behaviour of polyadenine in water based on a time-dependent density functional calculations. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9931-9966.
34. Tonzani, S.; Schatz, G. C. Electronic excitations and spectra in single-stranded DNA. J. Am. Chem. Soc. 2008, 130, 7607-7612; see also their supplementary material.
35. Zerner, M. C.; Loew, G. H.; Kirchner, R. F.; Mueller-Westerhoff, U. T. An intermediate neglect of differential overlap technique for spectroscopy of transition-metal complexes. Ferrocene. J. Am. Chem. Soc. 1980, 102, 589-599.
36. Thompson, M. A. QM/MMpol: A Consistent Model for Solute/Solvent Polarization. Application to the Aqueous Solvation and Spectroscopy of Formaldehyde, Acetaldehyde, and Acetone. J. Phys. Chem. 1996, 100, 14492-14507.
37. Olson, W. K.; Bansal, M.; Burley, S. K.; Dickerson, R. E.; Gerstein, M.; Harvey, S. C.; Heinemann, U.; Lu, X. J.; Neidle, S.; Shakked, Z.; Sklenar, H.; Suzuki, M.; Tung, C. S.; Westhof, E.; Wolberger, C.; Berman, H. M. A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 2001, 313, 229-237.
38. Lu, X. J.; Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 2003, 31, 5108-5121.
39. Starikov, E. B. Electron-phonon coupling in DNA: A systematic study. Philos. Mag. 2005, 85, 3435-3462.
40. Shafranovskaya, N. N.; Trifonov, E. N.; Lazurkin, Yu. S.; Frank-Kamenetskii, M. D. JETP Lett. 1972, 15, 404-408.
41. Rahn, R. O.; Shulman, R. G.; Longworth, J. W. The UV-induced triplet state in DNA. Proc. Natl. Acad. Sci. U.S.A. 1965, 53, 893-896.
42. Crespo-Hernandez, C. E.; Cohen, B.; Kohler, B. Base stacking controls excited state dynamics in AT DNA. Nature 2005, 436, 1141-1144.
43. Volkenstein, M. V. The conformon. J. Theor. Biol. 1972, 35, 193-195.
44. Volkenstein, M. V.; Golovanov, I. B.; Sobolev, V. M. Electron- conformational interactions and functioning of enzyme molecules. Int. J. Quantum Chem. 1979, 16, 777-789.
45. Bersuker, I. B. QSAR without arbitrary descriptors: The electron-conformational method. J. Comput. Aided Mol. Des. 2008, 22, 423-430.
46. Luchowski, R.; Krawczyk, S. Electroabsorption (Stark effect) spectroscopy of monomeric purine and pyrimidine bases. Chem. Phys. 2005, 314, 309-316.