Electronic deactivation of guanosine in extended hydrogen-bonded self-assemblies

Journal of Physical Chemistry A

Volumn 117, Issue 12, 2013, Pages 2469-2478

  Röttger, Katharina ^a   Schwalb, Nina K ^a   Temps, Friedrich ^a  

^a UNIVERSITY OF KIEL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULES; BRIDGE CIRCUITS; DIMERS; HEXANE; HYDROGEN; HYDROGEN BONDS; MOLECULES; NETWORK ARCHITECTURE; POTENTIAL ENERGY; SUPRAMOLECULAR CHEMISTRY; THALLIUM ALLOYS;

DEACTIVATION PATHWAYS; ELECTRONIC RELAXATION; EXCITED ELECTRONIC STATE; EXCITED STATE LIFETIMES; FEMTOSECOND FLUORESCENCE; RADIATIONLESS DEACTIVATION; SUPRAMOLECULAR ARCHITECTURES; SUPRAMOLECULAR NETWORKS;

EXCITED STATES;

EID: 84875701873     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp3095193     Document Type: Article

References (76)

1. Gellert, M.; Lipsett, M. N.; Davies, D. R. Helix Formation of Guanylic Acid Proc. Natl. Acad. Sci. U.S.A. 1962, 48, 2013-2018
2. Guschlbauer, W.; Chantot, J.-F.; Thiele, D. Four-Stranded Nucleic Acid Structures 25 Years Later: From Guanosine Gels to Telomer DNA J. Biomol. Struct. Dyn. 1990, 8, 491-511
3. Davis, J. T. Angew. Chem., Int. Ed. 2004, 43, 668-698
4. Mills, M.; Lacroix, L.; Arimondo, P. B.; Leroy, J.-L.; François, J.-C.; Klump, H.; Mergny, J. L. G-Quartets 40 Years Later: From 5′-GMP to Molecular Biology and Supramolecular Chemistry Curr. Med. Chem.-Anti-Cancer Agents 2002, 2, 627-644
5. Williamson, J. R. Unusual DNA Conformations: Implications for Telomeres Annu. Rev. Biophys. Biomol. Struct. 1994, 23, 703-730
6. Bloomfield, V. A.; Crothers, D. M.; Tinoco, I. Nucleic Acids: Structures, Properties and Functions; University Science Books: Sausalito, CA, 2000.
7. Bianchi, A.; Shore, D. Telomeres: Maintenance and Replication. In Encyclopedia of Biological Chemistry; Lennarz, W. J.; Lane, M. D., Eds.; Elsevier: Amsterdam, 2004; Vol. 4.
8. De Cian, A.; Lacroix, L.; Douarre, C.; Temime-Smaali, N.; Trentesaux, C.; Riou, J.-F.; Mergny, J.-L. Targeting Telomeres and Telomerase Biochimie 2008, 90, 131-155 (Pubitemid 350245369)
9. Worlinsky, J. L.; Basu, S. Detection of Quadruplex DNA by Luminescence Enhancement of Lanthanide Ions and Energy Transfer from Lanthanide Chelates J. Phys. Chem. B 2009, 113, 865-868
10. Davis, J. T.; Spada, G. P. Supramolecular Architectures Generated by Self-Assembly of Guanosine Derivatives Chem. Soc. Rev. 2007, 36, 296-313
11. Rinaldi, R.; Maruccio, G.; Biasco, A.; Arima, V.; Cingolani, R.; Giorgi, T.; Masiero, S.; Spada, G. P.; Gottarelli, G. Molecular Electronic Devices Based on Modified Deoxyguanosines Nanotechnology 2002, 13, 398-403 (Pubitemid 34711892)
12. Nir, E.; Janzen, C.; Imhof, P.; Kleinermanns, K.; de Vries, M. S. Pairing of the Nucleobase Guanine Studied by IR-UV Double-Resonance Spectroscopy and Ab Initio Calculations Phys. Chem. Chem. Phys. 2002, 4, 740-750
13. Gottarelli, G.; Masiero, S.; Mezzina, E.; Spada, G. P.; Mariani, P.; Recanatini, M. The Self-Assembly of a Lipophilic Deoxyguanosine Derivative and the Formation of a Liquid-Crystalline Phase in Hydrocarbon Solvents Helv. Chim. Acta 1998, 81, 2078-2092 (Pubitemid 28536385)
14. Giorgi, T.; Grepioni, F.; Manet, I.; Mariani, P.; Masiero, S.; Mezzina, E.; Pieraccini, S.; Saturni, L.; Spada, G. P.; Gottarelli, G. Gel-Like Lyomesophases Formed in Organic Solvents by Self-Assembled Guanine Ribbons Chem.-Eur. J. 2002, 8, 2143-2152 (Pubitemid 34534438)
15. Sessler, J. L.; Sathiosatham, M.; Doerr, K.; Lynch, V.; Abboud, K. A. A G-Quartet Formed in the Absence of a Templating Metal Cation: A New (N,N-Dimethylaniline)guanosine Derivative Angew. Chem., Int. Ed. 2000, 39, 1300-1303 (Pubitemid 30219936)
16. Giorgi, T.; Lena, S.; Mariani, P.; Cremonini, M. A.; Masiero, S.; Pieraccini, S.; Rabe, J. P.; Samor, P.; Spada, G. P.; Gottarelli, G. Supramolecular Helices via Self-Assembly of 8-Oxoguanosines J. Am. Chem. Soc. 2003, 125, 14741-14749 (Pubitemid 37475565)
17. 3T) Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 8832-8836
18. van Mourik, T.; Dingley, A. J. Characterization of the Monovalent Ion Position and Hydrogen-Bond Network in Guanine Quartets by DFT Calculations of NMR Parameters Chem.-Eur. J. 2005, 11, 6064-6079 (Pubitemid 41454706)
19. Romero Guzmán, M.; Liquier, J.; Brahmachari, S. K.; Taillandier, E. Characterization of Parallel and Antiparallel G-Tetraplex Structures by Vibrational Spectroscopy Spectrochim. Acta A 2006, 64, 495-503
20. González-Rodrguez, D.; van Dongen, J. L. J.; Lutz, M.; Spek, A. L.; Schenning, A. P. H. J.; Meijer, E. W. G-Quadruplex Self-Assembly Regulated by Coulombic Interactions Nat. Chem. 2009, 1, 151-155
21. Vglaský, V.; Bauer, L.; Tluc̆ková, K. Structural Features of Intra- and Intermolecular G-Quadruplexes Derived from Telomeric Repeats Biochemistry 2010, 49, 2110-2120
22. Masiero, S.; Trotta, R.; Pieraccini, S.; De Tito, S.; Perone, R.; Randazzo, A.; Spada, G. P. Non-Empirical Chromophoric Interpretation of CD Spectra of DNA G-Quadruplex Structures Org. Biomol. Chem. 2010, 8, 2683-2692
23. Miannay, F.-A.; Banyasz, A.; Gustavsson, T.; Markovitsi, D. Excited States and Energy Transfer in G-Quadruplexes J. Phys. Chem. C 2009, 113, 11760-11765
24. Changenet-Barret, P.; Emanuele, E.; Gustavsson, T.; Improta, R.; Kotlyar, A. B.; Markovitsi, D.; Vayá, I.; Zakrzewska, K.; Zikich, D. Optical Properties of Guanine Nanowires: Experimental and Theoretical Study J. Phys. Chem. C 2010, 114, 14339-14346
25. Hua, Y.; Changenet-Barret, P.; Improta, R.; Vayá, I.; Gustavsson, T.; Kotlyar, A. B.; Zikich, D.; Šket, P.; Plavec, J.; Markovitsi, D. Cation Effect on the Electronic Excited States of Guanine Nanostructures Studied by Time-Resolved Fluorescence Spectroscopy J. Phys. Chem. C 2012, 116, 14682-14689
26. 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 (Pubitemid 47218781)
27. Schwalb, N. K.; Michalak, T.; Temps, F. Ultrashort Fluorescence Lifetimes of Hydrogen-Bonded Guanosine and Cytidine Containing Base Pairs in Solution J. Phys. Chem. B 2009, 113, 16365-16376
28. Yang, M.; Szyc, L.; Röttger, K.; Fidder, H.; Nibbering, E. T. J.; Elsaesser, T.; Temps, F. Dynamics and Couplings of N-H Stretching Excitations of Guanosine-Cytidine Base Pairs in Solution J. Phys. Chem. B 2011, 115, 5484-5492
29. Fidder, H.; Yang, M.; Nibbering, E. T. J.; Elsaesser, T.; Röttger, K.; Temps, F. N-H Stretching Vibrations of Guanosine-Cytidine Base Pairs in Solution: Ultrafast Dynamics, Couplings and Lineshapes J. Phys. Chem. A 2013, 117, 845-854
30. Mariani, P.; Spinozzi, F.; Federiconi, F.; Amenitsch, H.; Spindler, L.; Drevensek-Olenik, I. Small Angle X-ray Scattering Analysis of Deoxyguanosine 5′-Monophosphate Self-Assembling in Solution: Nucleation and Growth of G-Quadruplexes J. Phys. Chem. B 2009, 113, 7934-7944
31. Crespo-Hernández, C. E.; Cohen, B.; Hare, P. M.; Kohler, B. Ultrafast Excited-State Dynamics in Nucleic Acids Chem. Rev. 2004, 104, 1977-2019
32. Schwalb, N. K.; Temps, F. Base Sequence and Higher-Order Structure Induce the Complex Excited-State Dynamics in DNA Science 2008, 322, 243-245
33. Serrano-Andrés, L.; Merchán, M. Are the Five Natural DNA/RNA Base Monomers a Good Choice from Natural Selection? A Photochemical Perspective J. Photochem. Photobiol. C 2009, 10, 21-32
34. Middleton, C. T.; de La Harpe, K.; Su, C.; Law, Y. K.; Crespo-Hernández, C. E.; Kohler, B. DNA Excited-State Dynamics: From Single Bases to the Double Helix Annu. Rev. Phys. Chem. 2009, 60, 217-239
35. Gustavsson, T.; Improta, R.; Markovitsi, D. DNA/RNA: Building Blocks of Life Under UV Irradiation J. Phys. Chem. Lett. 2010, 1, 2025-2030
36. Sobolewski, A. L.; Domcke, W. Ab Initio Studies on the Photophysics of the Guanine-Cytosine Base Pair Phys. Chem. Chem. Phys. 2004, 6, 2763-2771
37. Sobolewski, A. L.; Domcke, W.; Hättig, C. Tautomeric Selectivity of the Excited-State Lifetime of Guanosine/Cytosine Base Pairs: The Role of Electron-Driven Proton Transfer Processes Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 17903-17906 (Pubitemid 41798474)
38. Perun, S.; Sobolewski, A.; Domcke, W. Role of Electron-Driven Proton-Transfer in the Excited-State Deactivation of the Adenine-Thymine Base Pair J. Phys. Chem. A 2006, 110, 9031-9038 (Pubitemid 44187325)
39. Abo-Riziq, A.; Grace, L.; Nir, E.; Kabeláč, M.; Hobza, P.; de Vries, M. S. Photochemical Selectivity in Guanine-Cytosine Base-Pair Structures Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 20-23 (Pubitemid 40094421)
40. Samoylova, E.; Lippert, H.; Ullrich, S.; Hertel, I. V.; Radloff, W.; Schulz, T. Dynamics of Photoinduced Processes in Adenine and Thymine Base Pairs J. Am. Chem. Soc. 2005, 127, 1782-1786 (Pubitemid 40229161)
41. Schwalb, N. K.; Temps, F. On the Structure and Excited Electronic State Lifetimes of Cytidine Self-Assemblies with Extended Hydrogen-Bonding Networks J. Photochem. Photobiol. A 2009, 208, 164-170
42. Ogilvie, K. K. The tert -Butyldimethylsilyl Group as a Protecting Group in Deoxynucleosides Can. J. Chem. 1973, 51, 3799-3807
43. Pancur, T.; Schwalb, N. K.; Renth, F.; Temps, F. Femtosecond Fluorescence Up-Conversion Spectroscopy of Adenine and Adenosine: Experimental Evidence for the πσ* State? Chem. Phys. 2005, 313, 199-212 (Pubitemid 40501955)
44. 6-Dimethyladenine Derived from Femtosecond Fluorescence Spectroscopy J. Phys. Chem. A 2009, 113, 13113-13123
45. Röttger, K.; Siewertsen, R.; Temps, F. Ultrafast Electronic Deactivation Dynamics of the Rare Natural Nucleobase Hypoxanthine Chem. Phys. Lett. 2012, 536, 140-146
46. Lorenc, M.; Ziolek, M.; Naskrecki, R.; Karolczak, J.; Kubicki, J.; Maciejewski, A. Artifacts in Femtosecond Transient Absorption Spectroscopy Appl. Phys. B: Lasers Opt. 2002, 74, 19-27 (Pubitemid 41200780)
47. Dobryakov, A. L.; Kovalenko, S. A.; Ernsting, N. P. Electronic and Vibrational Coherence Effects in Broadband Transient Absorption Spectroscopy with Chirped Supercontinuum Probing J. Chem. Phys. 2003, 119, 988-1002
48. Dobryakov, A. L.; Kovalenko, S. A.; Ernsting, N. P. Coherent and Sequential Contributions to Femtosecond Transient Absorption Spectra of a Rhodamine Dye in Solution J. Chem. Phys. 2005, 123, 044502
49. LabView 8.0; National Instruments: 2006.
50. Mathematica Version 8.0; Wolfram Research, Inc.: 2011.
51. Schönborn, J. B. unpublished results.
52. Trantrek, L.; Štefl, R.; Vorlc̆ková, M.; Koc̆a, J.; Sklenář, V.; Kypr, J. An A-Type Double Helix of DNA Having B-Type Puckering of the Deoxyribose Rings J. Mol. Biol. 2000, 297, 907-922
53. Štefl, R.; Trantírek, L.; Vorlíc̆ ková, M.; Koc̆a, J.; Sklenář, V.; Kypr, J. A-Like Guanine-Guanine Stacking in Aqueous DNA of d(GGGGCCCC) J. Mol. Biol. 2001, 307, 513-524 (Pubitemid 33027675)
54. Barbatti, M.; Lischka, H. Nonadiabatic Deactivation of 9H-Adenine: A Comprehensive Picture Based on Mixed Quantum-Classical Dynamics J. Am. Chem. Soc. 2008, 130, 6831-6839 (Pubitemid 351748421)
55. Barbatti, M.; Aquino, A. J. A.; Szymczak, J. J.; Nachtigallová, D.; Hobza, P.; Lischka, H. Relaxation Mechanisms of UV-Photoexcited DNA and RNA Nucleobases Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 21453-21458
56. Barbatti, M.; Szymczak, J. J.; Aquino, A. J. A.; Nachtigallová, D.; Lischka, H. The Decay Mechanism of Photoexcited Guanine-A Nonadiabatic Dynamics Study J. Chem. Phys. 2011, 134, 014304
57. 2 Excitonic Splittings and Vibronic Coupling in the Excited State of the Jet-Cooled 2-Aminopyridine Dimer J. Chem. Phys. 2009, 131, 204308
58. 2 Exciton Interaction in 2-Pyridone·6-Methyl-2- pyridone: Davydov Splitting, Vibronic Coupling, and Vibronic Quenching J. Chem. Phys. 2011, 135, 154311
59. Ottiger, P.; Leutwyler, S.; Köppel, H. Vibrational Quenching of Excitonic Splittings in HBonded Molecular Dimers: The Electronic Davydov Splittings Cannot Match Experiment J. Chem. Phys. 2012, 136, 174308
60. Kopec, S.; Ottiger, P.; Leutwyler, S.; Köppel, H. Vibrational Quenching of Excitonic Splittings in H-Bonded Molecular Dimers: Adiabatic Description and Effective Mode Approximation J. Chem. Phys. 2012, 137, 184312
61. Elsaesser, T.; Kaiser, W. Vibrational and Vibronic Relaxation of Large Polyatomic Molecules in Liquids Annu. Rev. Phys. Chem. 1991, 42, 83-107
62. Kang, H.; Lee, K. T.; Jung, B.; Ko, Y. J.; Kim, S. K. Intrinsic Lifetimes of the Excited State of DNA and RNA Bases J. Am. Chem. Soc. 2002, 124, 12958-12959 (Pubitemid 35247102)
63. Canuel, C.; Mons, M.; Piuzzi, F.; Tardivel, B.; Dimicoli, I.; Elhanine, M. Excited States Dynamics of DNA and RNA Bases: Characterization of a Stepwise Deactivation Pathway in the Gas Phase J. Chem. Phys. 2005, 122, 074316
64. Peon, J.; Zewail, A. H. DNA/RNA Nucleotides and Nucleosides: Direct Measurement of Excited-State Lifetimes by Femtosecond Fluorescence Up-Conversion Chem. Phys. Lett. 2001, 348, 255-262 (Pubitemid 33630861)
65. Pecourt, J.-M. L.; Peon, J.; Kohler, B. DNA Excited-State Dynamics: Ultrafast Internal Conversion and Vibrational Cooling in a Series of Nucleosides J. Am. Chem. Soc. 2001, 123, 10370-10378 (Pubitemid 32979787)
66. Karunakaran, V.; Kleinermanns, K.; Improta, R.; Kovalenko, S. A. Photoinduced Dynamics of Guanosine Monophosphate in Water from Broad-Band Transient Absorption Spectroscopy and Quantum-Chemical Calculations J. Am. Chem. Soc. 2009, 131, 5839-5850
67. Miannay, F.-A.; Gustavsson, T.; Bányász, A.; Markovitsi, D. Excited-State Dynamics of dGMP Measured by Steady-State and Femtosecond Fluorescence Spectroscopy J. Phys. Chem. A 2010, 114, 3256-3263
68. Chen, H.; Li, S. Ab Initio Study on Deactivation Pathways of Excited 9H-Guanine J. Chem. Phys. 2006, 124, 154315
69. Marian, C. M. The Guanine Tautomer Puzzle: Quantum Chemical Investigation of Ground and Excited States J. Phys. Chem. A 2007, 111, 1545-1553 (Pubitemid 46463844)
70. Yamazaki, S.; Domcke, W. Ab Initio Studies on the Photophysics of Guanine Tautomers: Outof-Plane Deformation and NH Dissociation Pathways to Conical Intersections J. Phys. Chem. A 2008, 112, 7090-7097
71. Yamazaki, S.; Domcke, W.; Sobolewski, A. L. Nonradiative Decay Mechanisms of the Biologically Relevant Tautomer of Guanine J. Phys. Chem. A 2008, 112, 11965-11968
72. Serrano-Andrés, L.; Merchán, M.; Borin, A. C. A Three-State Model for the Photophysics of Guanine J. Am. Chem. Soc. 2008, 130, 2473-2484 (Pubitemid 351307797)
73. Lan, Z.; Fabiano, E.; Thiel, W. Photoinduced Nonadiabatic Dynamics of 9H-Guanine ChemPhysChem 2009, 10, 1225-1229
74. Candeias, L. P.; Steenken, S. Structure and Acid-Base Properties of One-Electron-Oxidized Deoxyguanosine, Guanosine, and 1-Methylguanosine J. Am. Chem. Soc. 1989, 111, 1094-1099 (Pubitemid 19053424)
75. Jian, L.; Wang, W.-F.; Zheng, Z.-D.; Yao, S.-D.; Zhang, J.-S.; Lin, N.-Y. Reactive Intermediates in Laser Photolysis of Guanosine Res. Chem. Intermed. 1991, 15, 293-301
76. Wood, P. D.; Redmond, R. W. Triplet State Interactions between Nucleic Acid Bases in Solution at Room Temperature: Intermolecular Energy and Electron Transfer J. Am. Chem. Soc. 1996, 118, 4256-4263 (Pubitemid 26167545)