Photoinduced electron transfer occurs between 2-aminopurine and the DNA nucleic acid monophosphates: Results from cyclic voltammetry and fluorescence quenching

Journal of Physical Chemistry B

Volumn 114, Issue 32, 2010, Pages 10573-10580

  Narayanan, Madhavan ^a   Kodali, Goutham ^a   Xing, Yangjun ^a   Stanley, Robert J ^a  

^a Temple University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC VOLTAMMETRY; DNA; ELECTRON TRANSITIONS; FLUORESCENCE; GENES; NUCLEIC ACIDS; ORGANIC SOLVENTS; RATE CONSTANTS;

2-AMINOPURINE; 2-AMINOPURINE (2AP); APROTIC; AQUEOUS SOLUTIONS; BASE STACKING; ELECTRON ACCEPTOR; ELECTRON DONORS; FLUORESCENCE QUANTUM YIELD; FLUORESCENCE QUENCHING; MONOPHOSPHATES; OXIDATION POTENTIALS; PHOTO-INDUCED ELECTRON TRANSFER; QUENCHING MECHANISMS; QUENCHING RATE CONSTANT; SEQUENCE-DEPENDENT; SPECTROSCOPIC DATA; STERN-VOLMER;

QUENCHING;

EID: 84962388429     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp102355v     Document Type: Article

References (59)

1. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. J. Physical chemistry of nucleic acids; Harper and Row: New York, 1974.
2. Santalucia, J., Jr. The use of spectroscopic techniques in the study of DNA stability. In Spectrophotometry and Spectrofluorimetry, 2nd ed.; Oxford University Press: New York, 2000; pp 329 - 356.
3. Peon, J.; Zewail, A. H. DNA/RNA nucleotides and nucleosides: direct measurement of excited-state lifetimes by femto-second fluorescence up-conversion Chem. Phys. Lett. 2001, 348 (3,4) 255-262
4. Gustavsson, T.; Sharonov, A.; Markovitsi, D. Thymine, thymidine and thymidine 5′-monophosphate studied by femtosecond fluorescence upconversion spectroscopy Chem. Phys. Lett. 2002, 351 (3,4) 195-200
5. Gustavsson, T.; Sharonov, A.; Onidas, D.; Markovitsi, D. Adenine, deoxyadenosine and deoxyadenosine 5′-monophosphate studied by femtosecond fluorescence upconversion spectroscopy Chem. Phys. Lett. 2002, 356 (1,2) 49-54
6. Cohen, B.; Hare, P. M.; Kohler, B. Ultrafast Excited-State Dynamics of Adenine and Monomethylated Adenines in Solution: Implications for the Nonradiative Decay Mechanism J. Am. Chem. Soc. 2003, 125 (44) 13594-13601
7. Crespo-Hernandez, C. E.; Cohen, B.; Hare, P. M.; Kohler, B. Ultrafast Excited-State Dynamics in Nucleic Acids Chem. Rev. 2004, 104 (4) 1977-2019
8. Reuther, A.; Nikogosyan, D. N.; Laubereau, A. Primary Photochemical Processes in Thymine in Concentrated Aqueous Solution Studied by Femtosecond UV Spectroscopy J. Phys. Chem. 1996, 100 (13) 5570-5577
9. Yarkony, D. R. Conical Intersections: The New Conventional Wisdom J. Phys. Chem. A 2001, 105 (26) 6277-6293
10. Matsika, S. Conical intersections in molecular systems Rev. Comput. Chem. 2007, 23, 83-124
11. Domcke, W.; Yarkony, D. R.; Koppel, H. Conical Intersections: Electronic Structure, Dynamics, and Spectroscopy; World Scientific Publishing Co.: Hackensack, NJ, 2004.
12. Ward, D. C.; Reich, E.; Stryer, L. Fluorescence Studies of Nucleotides and Polynucleotides J. Biol. Chem. 1969, 244 (5) 1228-1237
13. Nordlund, T. M.; Andersson, S.; Nilsson, L.; Rigler, R.; Graeslund, A.; McLaughlin, L. W. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies Biochemistry 1989, 28 (23) 9095-9103
14. Evans, K.; Xu, D.; Kim, Y.; Nordlund, T. M. 2-Aminopurine optical spectra: solvent, pentose ring, and DNA helix melting dependence J. Fluoresc. 1992, 2 (4) 209-216
15. Nordlund, T. M.; Xu, D.; Evans, K. O. Excitation energy transfer in DNA: Duplex melting and transfer from normal bases to 2-aminopurine Biochemistry 1993, 32 (45) 12090-12095
16. Guest, C. R.; Hochstrasser, R. A.; Sowers, L. C.; Millar, D. P. Dynamics of mismatched base pairs in DNA Biochemistry 1991, 30 (13) 3271-3279
17. Xu, D.; Evans, K. O.; Nordlund, T. M. Melting and Premelting Transitions of an Oligomer Measured by DNA Base Fluorescence and Absorption Biochemistry 1994, 33 (32) 9592-9529
18. Law, S. M.; Eritja, R.; Goodman, M. F.; Breslauer, K. J. Spectroscopic and Calorimetric Characterizations of DNA Duplexes Containing 2-Aminopurine Biochemistry 1996, 35 (38) 12329-12337
19. Bloom, L. B.; Otto, M. R.; Eritja, R.; Reha-Krantz, L. J.; Goodman, M. F.; Beechem, J. M. Pre-Steady-State Kinetic Analysis of Sequence-Dependent Nucleotide Excision by the 3′-Exonuclease Activity of Bacteriophage T4 DNA Polymerase Biochemistry 1994, 33 (24) 7576-7586
20. Raney, K. D.; Sowers, L. C.; Millar, D. P.; Benkovic, S. J. A fluorescence-based assay for monitoring helicase activity Proc. Natl. Acad. Sci. U.S.A. 1994, 91 (14) 6644-6648
21. Frey, M. W.; Sowers, L. C.; Millar, D. P.; Benkovic, S. J. The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase Biochemistry 1995, 34 (28) 9185-9192
22. Allan, B. W.; Reich, N. O. Targeted base stacking disruption by the EcoRI DNA methyltransferase Biochemistry 1996, 35 (47) 14757-14762
23. McCullough, A. K.; Dodson, M. L.; Scharer, O. D.; Lloyd, R. S. The role of base flipping in damage recognition and catalysis by T4 endonuclease V J. Biol. Chem. 1997, 272 (43) 27210-27217
24. Allan, B. W.; Beechem, J. M.; Lindstrom, W. M.; Reich, N. O. Direct real time observation of base flipping by the EcoRI DNA methyltransferase J. Biol. Chem. 1998, 273 (4) 2368-2373
25. Holz, B.; Klimasauskas, S.; Serva, S.; Weinhold, E. 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases Nucleic Acids Res. 1998, 26 (4) 1076-1083
26. Stivers, J. T.; Pankiewicz, K. W.; Watanabe, K. A. Kinetic Mechanism of Damage Site Recognition and Uracil Flipping by Escherichia coli Uracil DNA Glycosylase Biochemistry 1999, 38 (3) 952-963
27. Christine, K. S.; MacFarlane, A. W., IV; Yang, K.; Stanley, R. J. Cyclobutylpyrimidine Dimer Base Flipping by DNA Photolyase J. Biol. Chem. 2002, 277 (41) 38339-38344
28. Yang, K.; Stanley, R. J. Differential Distortion of Substrate Occurs When It Binds to DNA Photolyase: A 2-Aminopurine Study Biochemistry 2006, 45 (37) 11239-11245
29. Fiebig, T.; Wan, C.; Zewail, A. H. Femtosecond charge transfer dynamics of a modified DNA base: 2-aminopurine in complexes with nucleotides ChemPhysChem 2002, 3 (9) 781-788
30. Larsen, O. F. A.; van Stokkum, I. H. M.; de Weerd, F. L.; Vengris, M.; Aravindakumar, C. T.; van Grondelle, R.; Geacintov, N. E.; van Amerongen, H. Ultrafast transient-absorption and steady-state fluorescence measurements on 2-aminopurine substituted dinucleotides and 2-aminopurine substituted DNA duplexes Phys. Chem. Chem. Phys. 2004, 6 (1) 154-160
31. Somsen, O. J. G.; Van Hoek, A.; Van Amerongen, H. Fluorescence quenching of 2-aminopurine in dinucleotides Chem. Phys. Lett. 2005, 402 (1-3) 61-65
32. Bierzynski, A.; Kozlowska, H.; Wierzchowski, K. L. Investigations on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method. II. Heteroassociation between 2-aminopurine and thymidine Biophys. Chem. 1977, 6 (3) 223-229 (Pubitemid 8122524)
33. Bierzynski, A.; Kozlowska, H.; Wierzchowski, K. L. Investigation on purine and pyrimidine bases stacking associations in aqueous solutions by the fluorescence quenching method. I. Autoassociation of 2-aminopurine Biophys. Chem. 1977, 6 (3) 213-222 (Pubitemid 8122523)
34. Kelley, S. O.; Barton, J. K. Electron transfer between bases in double helical DNA Science (Washington, D.C.) 1999, 283 (5400) 375-381
35. Reynisson, J.; Steenken, S. One-electron reduction of 2-aminopurine in the aqueous phase. A DFT and pulse radiolysis study Phys. Chem. Chem. Phys. 2005, 7 (4) 659-665
36. Marcus, R. A.; Sutin, N. Electron transfers in chemistry and biology Biochim. Biophys. Acta 1985, 811 (3) 265-322
37. Yao, T.; Musha, S. The electrochemical oxidation of aminopurines and their hydroxy derivatives at the glassy carbon electrode Bull. Chem. Soc. Jpn. 1979, 52 (8) 2307-11
38. Lakowicz, J. R. Principles of Fluorescence Spectroscopy, 3rd ed.; Springer: New York, 2006.
39. Rehm, D.; Weller, A. Kinetics of Fluorescence Quenching by Electron and H-Atom Transfer Isr. J. Chem. 1970, 8, 259-271
40. Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. Nucleobase-Specific Quenching of Fluorescent Dyes. 1. Nucleobase One-Electron Redox Potentials and Their Correlation with Static and Dynamic Quenching Efficiencies J. Phys. Chem. 1996, 100 (13) 5541-5553
41. Narayanan, M.; Kodali, G.; Xing, Y.; Hawkins, M. E.; Stanley, R. J. Differential Fluorescence Quenching of Fluorescent Nucleic Acid Base Analogues by Native Nucleic Acid Monophosphates J. Phys. Chem. B 2010, 114 (17) 5953-5963
42. Cavaluzzi, M. J.; Borer, P. N. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA Nucleic Acids Res. 2004, 32 (1) 1-9
43. Smagowicz, J.; Wierzchowski, K. L. Lowest excited states of 2-aminopurine J. Lumin. 1974, 8 (3) 210-232
44. Pavlishchuk, V. V.; Addison, A. W. Conversion constants for redox potentials measured versus different reference electrodes in acetonitrile solutions at 25°C Inorg. Chim. Acta 2000, 298, 97-102
45. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, N. K.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision A.1; Gaussian, Inc.: Pittsburgh, PA, 2003.
46. Boäes, E. S.; Livotto, P. R.; Stassen, H. Solvation of monovalent anions in acetonitrile and N, N-dimethylformamide: Parameterization of the IEF-PCM model Chem. Phys. 2006, 331, 142-158
47. Miertus, S.; Scrocco, E.; Tomasi, J. Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects Chem. Phys. 1981, 55 (1) 117-129
48. Miertus, S.; Tomasi, J. Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes Chem. Phys. 1982, 65 (2) 239-245
49. Pascual-Ahuir, J. L.; Silla, E.; Tomasi, J.; Bonaccorsi, R. Electrostatic interaction of a solute with a continuum. Improved description of the cavity and of the surface cavity bound charge distribution J. Comput. Chem. 2004, 8 (6) 778-787
50. Bharill, S.; Sarkar, P.; Ballin, J. D.; Gryczynski, I.; Wilson, G. M.; Gryczynski, Z. Fluorescence intensity decays of 2-aminopurine solutions: Lifetime distribution approach Anal. Biochem. 2008, 377 (2) 141-149
51. Pandey, A.; Datta, S. N. Theoretical Determination of Standard Oxidation and Reduction Potentials of Chlorophyll-a in Acetonitrile J. Phys. Chem. B 2005, 109 (18) 9066-9072
52. Kavarnos, G. J. Fundamentals of photoinduced electron transfer; VCH Publishers, Inc.: New York, 1993.
53. Crespo-Hernández, C. E.; Close, D. M.; Gorb, L.; Leszczynski, J. Determination of redox potentials for the Watson-Crick base pairs, DNA nucleosides, and relevant nucleoside analogues J. Phys. Chem. B 2007, 111 (19) 5386-5395
54. Stivers, J. T. 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects Nucleic Acids Res. 1998, 26 (16) 3837-3844
55. Rachofsky, E. L.; Osman, R.; Ross, J. B. A. Probing Structure and Dynamics of DNA with 2-Aminopurine: Effects of Local Environment on Fluorescence Biochemistry 2001, 40 (4) 946-956
56. Sutin, N. Theory of electron transfer reactions: insights and hindsights Prog. Inorg. Chem. 1983, 30, 441-498
57. Parsons, W. W. Modern Optical Spectroscopy; Springer: Berlin, Heidelberg, 2007.
58. Eberson, L. Electron-transfer reactions in organic chemistry Adv. Phys. Org. Chem. 1982, 18, 79-185
59. Holmen, A.; Norden, B.; Albinsson, B. Electronic transition moments of 2-aminopurine J. Am. Chem. Soc. 1997, 119 (13) 3114-3121