Hole transfer kinetics of DNA

Accounts of Chemical Research

Volumn 46, Issue 11, 2013, Pages 2616-2625

  Kawai, Kiyohiko ^a   Majima, Tetsuro ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BASE MISPAIRING; CHEMISTRY; CONFORMATION; KINETICS;

BASE PAIR MISMATCH; DNA; KINETICS; NUCLEIC ACID CONFORMATION;

EID: 84888590871     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar400079s     Document Type: Article

References (47)

1. Dohno, C.; Saito, I. Chemical Approach to Modulating Hole Transport Through DNA. In Charge Transfer in DNA; Wagenknecht, H.-A., Ed.; Wiley-VCH: Weinheim, 2005; pp 153-174.
2. Kelley, S. O.; Barton, J. K. Electron transfer between bases in double helical DNA Science 1999, 283, 375-381
3. Lewis, F. D.; Wu, T. F.; Zhang, Y. F.; Letsinger, R. L.; Greenfield, S. R.; Wasielewski, M. R. Distance-dependent electron transfer in DNA hairpins Science 1997, 277, 673-676
4. Wan, C. Z.; Fiebig, T.; Schiemann, O.; Barton, J. K.; Zewail, A. H. Femtosecond direct observation of charge transfer between bases in DNA Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 14052-14055
5. Gray, H. B.; Winkler, J. R. Long-range electron transfer Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 3534-3539
6. Davis, W. B.; Svec, W. A.; Ratner, M. A.; Wasielewski, M. R. Molecular-wire behavior in p-phenylenevinylene oligomers Nature 1998, 396, 60-63
7. Meggers, E.; Michel-Beyerle, M. E.; Giese, B. Sequence dependent long range hole transport in DNA J. Am. Chem. Soc. 1998, 120, 12950-12955
8. Henderson, P. T.; Jones, D.; Hampikian, G.; Kan, Y. Z.; Schuster, G. B. Long-distance charge transport in duplex DNA: The phonon-assisted polaron-like hopping mechanism Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 8353-8358
9. Misiaszek, R.; Crean, C.; Joffe, A.; Geacintov, N. E.; Shafirovich, V. Oxidative DNA damage associated with combination of guanine and superoxide radicals and repair mechanisms via radical trapping J. Biol. Chem. 2004, 279, 32106-32115
10. Osakada, Y.; Kawai, K.; Tachikawa, T.; Fujitsuka, M.; Tainaka, K.; Tero-Kubota, S.; Majima, T. Generation of singlet oxygen during photosensitized one-electron oxidation of DNA Chem.-Eur. J. 2012, 18, 1060-1063
11. Lewis, F. D.; Liu, X. Y.; Liu, J. Q.; Miller, S. E.; Hayes, R. T.; Wasielewski, M. R. Direct measurement of hole transport dynamics in DNA Nature 2000, 406, 51-53
12. Lewis, F. D.; Liu, J.; Zuo, X.; Hayes, R. T.; Wasielewski, M. R. Dynamics and energetics of single-step hole transport in DNA hairpins J. Am. Chem. Soc. 2003, 125, 4850-4861
13. Takada, T.; Kawai, K.; Fujitsuka, M.; Majima, T. Direct observation of hole transfer through double-helical DNA over 100 angstroms Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14002-14006
14. Takada, T.; Kawai, K.; Fujitsuka, M.; Majima, T. Contributions of the distance-dependent reorganization energy and proton-transfer to the hole-transfer process in DNA Chem.-Eur. J. 2005, 11, 3835-3842
15. Osakada, Y.; Kawai, K.; Fujitsuka, M.; Majima, T. Charge transfer through DNA nanoscaled assembly programmable with DNA building blocks Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 18072-18076
16. Osakada, Y.; Kawai, K.; Fujitsuka, M.; Majima, T. Kinetics of charge transfer in DNA containing a mismatch Nucleic Acids Res. 2008, 36, 5562-5570
17. Conron, S. M. M.; Thazhathveetil, A. K.; Wasielewski, M. R.; Burin, A. L.; Lewis, F. D. Direct Measurement of the Dynamics of Hole Hopping in Extended DNA G-Tracts. An Unbiased Random Walk J. Am. Chem. Soc. 2010, 132, 14388-14390
18. Thazhathveetil, A. K.; Trifonov, A.; Wasielewski, M. R.; Lewis, F. D. Increasing the Speed Limit for Hole Transport in DNA J. Am. Chem. Soc. 2011, 133, 11485-11487
19. Tainaka, K.; Fujitsuka, M.; Takada, T.; Kawai, K.; Majima, T. Sequence dependence of excess electron transfer in DNA J. Phys. Chem. B 2010, 114, 14657-14663
20. Park, M. J.; Fujitsuka, M.; Kawai, K.; Majima, T. Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA J. Am. Chem. Soc. 2011, 133, 15320-15323
21. Park, M. J.; Fujitsuka, M.; Nishitera, H.; Kawai, K.; Majima, T. Excess electron transfer dynamics in DNA hairpins conjugated with N,N- dimethylaminopyrene as a photosensitizing electron donor Chem. Commun. 2012, 48, 11008-11010
22. Kawai, K.; Takada, T.; Tojo, S.; Majima, T. Kinetics of weak distance-dependent hole transfer in DNA by adenine-hopping mechanism J. Am. Chem. Soc. 2003, 125, 6842-6843
23. Takada, T.; Kawai, K.; Cai, X.; Sugimoto, A.; Fujitsuka, M.; Majima, T. Charge separation in DNA via consecutive adenine hopping J. Am. Chem. Soc. 2004, 126, 1125-1129
24. Jortner, J.; Bixon, M.; Langenbacher, T.; Michel-Beyerle, M. E. Charge transfer and transport in DNA Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 12759-12765
25. Giese, B.; Amaudrut, J.; Kohler, A. K.; Spormann, M.; Wessely, S. Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling Nature 2001, 412, 318-320
26. Boon, E. M.; Ceres, D. M.; Drummond, T. G.; Hill, M. G.; Barton, J. K. Mutation detection by electrocatalysis at DNA-modified electrodes Nat. Biotechnol. 2000, 18, 1096-1100
27. Osakada, Y.; Kawai, K.; Majima, T. Kinetics of charge transfer through DNA across guanine-cytosine repeats intervened by adenine-thymine base pair(s) Bull. Chem. Soc. Jpn. 2013, 86, 25-30
28. Kravec, S. M.; Kinz-Thompson, C. D.; Conwell, E. M. Localization of a Hole on an Adenine-Thymine Radical Cation in B-Form DNA in Water J. Phys. Chem. B 2011, 115, 6166-6171
29. Venkatramani, R.; Keinan, S.; Balaeff, A.; Beratan, D. N. Nucleic acid charge transfer: Black, white and gray Coord. Chem. Rev. 2011, 255, 635-648
30. Renaud, N.; Berlin, Y. A.; Lewis, F. D.; Ratner, M. A. Between Superexchange and Hopping: An Intermediate Charge-Transfer Mechanism in Poly(A)-Poly(T) DNA Hairpins J. Am. Chem. Soc. 2013, 135, 3953-3963
31. Genereux, J. C.; Barton, J. K. Mechanisms for DNA Charge Transport Chem. Rev. 2010, 110, 1642-1662
32. Sugiyama, H.; Saito, I. Theoretical studies of GC-specific photocleavage of DNA via electron transfer: Significant lowering of ionization potential and 5′-localization of HOMO of stacked GG bases in B-form DNA J. Am. Chem. Soc. 1996, 118, 7063-7068
33. Kawai, K.; Hayashi, M.; Majima, T. HOMO energy gap dependence of hole-transfer kinetics in DNA J. Am. Chem. Soc. 2012, 134, 4806-4811
34. Wenger, O. S. How Donor-Bridge-Acceptor Energetics Influence Electron Tunneling Dynamics and Their Distance Dependences Acc. Chem. Res. 2011, 44, 25-35
35. Lewis, F. D.; Liu, J.; Weigel, W.; Rettig, W.; Kurnikov, I. V.; Beratan, D. N. Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12536-12541
36. Venkatramani, R.; Davis, K. L.; Wierzbinski, E.; Bezer, S.; Balaeff, A.; Keinan, S.; Paul, A.; Kocsis, L.; Beratan, D. N.; Achim, C.; Waldeck, D. H. Evidence for a Near-Resonant Charge Transfer Mechanism for Double-Stranded Peptide Nucleic Acid J. Am. Chem. Soc. 2011, 133, 62-72
37. Voityuk, A. A. Long-Range Electron Transfer in Biomolecules. Tunneling or Hopping? J. Phys. Chem. B 2011, 115, 12202-12207
38. Nakatani, K.; Dohno, C.; Saito, I. Modulation of DNA-mediated hole-transport efficiency by changing superexchange electronic interaction J. Am. Chem. Soc. 2000, 122, 5893-5894
39. Kawai, K.; Kodera, H.; Osakada, Y.; Majima, T. Sequence-independent and rapid long-range charge transfer through DNA Nat. Chem. 2009, 1, 156-159
40. Kawai, K.; Kodera, H.; Majima, T. Long-range charge transfer through DNA by replacing adenine with diaminopurine J. Am. Chem. Soc. 2010, 132, 627-630
41. Valis, L.; Wang, Q.; Raytchev, M.; Buchvarov, I.; Wagenknecht, H.-A.; Fiebig, T. Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 10192-10195
42. Grozema, F. C.; Tonzani, S.; Berlin, Y. A.; Schatz, G. C.; Siebbeles, L. D. A.; Ratner, M. A. Effect of Structural Dynamics on Charge Transfer in DNA Hairpins J. Am. Chem. Soc. 2008, 130, 5157-5166
43. Steinbrecher, T.; Koslowski, T.; Case, D. A. Direct Simulation of Electron Transfer Reactions in DNA Radical Cations J. Phys. Chem. B 2008, 112, 16935-16944
44. Kubar, T.; Elstner, M. Coarse-Grained Time-Dependent Density Functional Simulation of Charge Transfer in Complex Systems: Application to Hole Transfer in DNA J. Phys. Chem. B 2010, 114, 11221-11240
45. Bruylants, G.; Boccongelli, M.; Snoussi, K.; Bartik, K. Comparison of the Thermodynamics and Base-Pair Dynamics of a Full LNA:DNA Duplex and of the Isosequential DNA:DNA Duplex Biochemistry 2009, 48, 8473-8482
46. Kawai, K.; Hayashi, M.; Majima, T. Hole transfer in LNA and 5-me-2′-deoxyzebularine-modified DNA J. Am. Chem. Soc. 2012, 134, 9406-9409
47. Eichert, A.; Behling, K.; Betzel, C.; Erdmann, V. A.; Fuerste, J. P.; Foerster, C. The crystal structure of an 'All Locked' nucleic acid duplex Nucleic Acids Res. 2010, 38, 6729-6736