Donor/acceptor interactions in systematically modified RuII-OsII oligonucleotides

Journal of the American Chemical Society

Volumn 124, Issue 44, 2002, Pages 13231-13241

  Hurley, Dennis J ^a   Tor, Yitzhak ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIGID GEOMETRIES;

CARBON; CHROMOPHORES; DNA; ELECTRONS; ENERGY TRANSFER; LUMINESCENCE; MOLECULAR WEIGHT; QUENCHING;

BIOCHEMISTRY;

DOUBLE STRANDED DNA; NUCLEOSIDE; OLIGONUCLEOTIDE; OSMIUM; RUTHENIUM;

ARTICLE; CHEMICAL INTERACTION; CHEMICAL MODIFICATION; CHROMATOPHORE; ELECTRON TRANSPORT; ENERGY TRANSFER; STEADY STATE;

DNA; LUMINESCENT MEASUREMENTS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; ORGANOMETALLIC COMPOUNDS; OSMIUM; RUTHENIUM; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 0037032267     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja020172r     Document Type: Article

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18. Murphy, C. J.; Arkin, M. R.; Jenkins, Y.; Ghatlia, N. D.; Bossmann, S. H.; Turro, N. J.; Barton, J. K. Science 1993, 262, 1025-1029. Meade, T. J.; Kayyem, J. F. Angew. Chem., Int. Ed. Engl. 1995, 34, 352-354. Arkin, M. R.; Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K.; Hörmann, A.; Olson, E. J. C.; Barbara, P. F. Science 1996, 273, 475-480. Dandliker, P. J.; Holmlin, R. E.; Barton, J. K. Science 1997, 275, 1465-1468. Ortmans, I.; Content, S.; Boutonnet, N.; Kirsch-De Mesmaeker, A.; Bannwarth, W.; Constant, J.-F.; Defrancq, E.; Lhomme, J. Chem.-Eur. J. 1999, 5, 2712-2721. Núñez, M. E.; Hall, D. B.; Barton, J. K. Chem. Biol. 1999, 6, 85-97. Rack, J. J.; Krider, E. S.; Meade, T. J. J. Am. Chem. Soc. 2000, 122, 6287-6288. Tierney, M. T.; Sykora, M.; Khan, S. I.; Grinstaff, M. W. J. Phys. Chem. B 2000, 104, 7574-7576. Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K. Inorg. Chim. Acta 2000, 297, 88-97. Schiemann, O.; Turro, N. J.; Barton, J. K. J. Phys. Chem. B 2000, 104, 7214-7220. Williams, T. T.; Odom, D. T.; Barton, J. K. J. Am. Chem. Soc. 2000, 122, 9048-9049.
19. Murphy, C. J.; Arkin, M. R.; Jenkins, Y.; Ghatlia, N. D.; Bossmann, S. H.; Turro, N. J.; Barton, J. K. Science 1993, 262, 1025-1029. Meade, T. J.; Kayyem, J. F. Angew. Chem., Int. Ed. Engl. 1995, 34, 352-354. Arkin, M. R.; Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K.; Hörmann, A.; Olson, E. J. C.; Barbara, P. F. Science 1996, 273, 475-480. Dandliker, P. J.; Holmlin, R. E.; Barton, J. K. Science 1997, 275, 1465-1468. Ortmans, I.; Content, S.; Boutonnet, N.; Kirsch-De Mesmaeker, A.; Bannwarth, W.; Constant, J.-F.; Defrancq, E.; Lhomme, J. Chem.-Eur. J. 1999, 5, 2712-2721. Núñez, M. E.; Hall, D. B.; Barton, J. K. Chem. Biol. 1999, 6, 85-97. Rack, J. J.; Krider, E. S.; Meade, T. J. J. Am. Chem. Soc. 2000, 122, 6287-6288. Tierney, M. T.; Sykora, M.; Khan, S. I.; Grinstaff, M. W. J. Phys. Chem. B 2000, 104, 7574-7576. Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K. Inorg. Chim. Acta 2000, 297, 88-97. Schiemann, O.; Turro, N. J.; Barton, J. K. J. Phys. Chem. B 2000, 104, 7214-7220. Williams, T. T.; Odom, D. T.; Barton, J. K. J. Am. Chem. Soc. 2000, 122, 9048-9049.
20. Murphy, C. J.; Arkin, M. R.; Jenkins, Y.; Ghatlia, N. D.; Bossmann, S. H.; Turro, N. J.; Barton, J. K. Science 1993, 262, 1025-1029. Meade, T. J.; Kayyem, J. F. Angew. Chem., Int. Ed. Engl. 1995, 34, 352-354. Arkin, M. R.; Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K.; Hörmann, A.; Olson, E. J. C.; Barbara, P. F. Science 1996, 273, 475-480. Dandliker, P. J.; Holmlin, R. E.; Barton, J. K. Science 1997, 275, 1465-1468. Ortmans, I.; Content, S.; Boutonnet, N.; Kirsch-De Mesmaeker, A.; Bannwarth, W.; Constant, J.-F.; Defrancq, E.; Lhomme, J. Chem.-Eur. J. 1999, 5, 2712-2721. Núñez, M. E.; Hall, D. B.; Barton, J. K. Chem. Biol. 1999, 6, 85-97. Rack, J. J.; Krider, E. S.; Meade, T. J. J. Am. Chem. Soc. 2000, 122, 6287-6288. Tierney, M. T.; Sykora, M.; Khan, S. I.; Grinstaff, M. W. J. Phys. Chem. B 2000, 104, 7574-7576. Stemp, E. D. A.; Holmlin, R. E.; Barton, J. K. Inorg. Chim. Acta 2000, 297, 88-97. Schiemann, O.; Turro, N. J.; Barton, J. K. J. Phys. Chem. B 2000, 104, 7214-7220. Williams, T. T.; Odom, D. T.; Barton, J. K. J. Am. Chem. Soc. 2000, 122, 9048-9049.
21. (a) Juris, A.; Balzani, V.; Barigelletti, F.; Campagna, S.; Belser, P.; Von Zelewsky, A. Coord. Chem. Rev. 1988, 84, 85-277.
22. (b) Sauvage, J.-P.; Collin, J.-P.; Chambron, J.-C.; Guillerez, S.; Coudret, C.; Balzani, V.; Barigelletti, F.; De Cola, L.; Flamigni, L. Chem. Rev. 1994, 94, 993-1019.
23. (d) Balzani, V.; Juris, A.; Venturi, M.; Campagna, S.; Serroni, S. Chem. Rev. 1996, 96, 759-833.
24. (e) Barigelletti, F.; Flamigni, L.; Collin, J.-P.; Sauvage, J.-P. Chem. Commun. 1997, 333-338.
25. For the original formulation of the Förster and Dexter mechanisms, see: (a) Förster, Th. Discuss. Faraday Soc. 1959, 27, 7-17. (b) Dexter, D. L. J. Chem. Phys. 1953, 21, 836-850.
26. For the original formulation of the Förster and Dexter mechanisms, see: (a) Förster, Th. Discuss. Faraday Soc. 1959, 27, 7-17. (b) Dexter, D. L. J. Chem. Phys. 1953, 21, 836-850.
27. For review articles, see: Barigelletti, F.; Flamigni, L. Chem. Soc. Rev. 2000, 29, 1-12. Ward, M. D.; Barigelletti, F. Coord. Chem. Rev. 2001, 216-217, 127-154.
28. For review articles, see: Barigelletti, F.; Flamigni, L. Chem. Soc. Rev. 2000, 29, 1-12. Ward, M. D.; Barigelletti, F. Coord. Chem. Rev. 2001, 216-217, 127-154.
29. Vögtle, F.; Frank, M.; Nieger, M.; Belser, P.; von Zelewsky, A.; Balzani, V.; Barigelletti, F.; De Cola, L.; Flamigni, L. Angew. Chem., Int. Ed. Engl. 1993, 32, 1643-1646. See also: Belser, P.; Dux, R.; Baak, M.; De Cola, L.; Balzani, V. Angew. Chem., Int. Ed. Engl. 1995, 34, 595-598.
30. Vögtle, F.; Frank, M.; Nieger, M.; Belser, P.; von Zelewsky, A.; Balzani, V.; Barigelletti, F.; De Cola, L.; Flamigni, L. Angew. Chem., Int. Ed. Engl. 1993, 32, 1643-1646. See also: Belser, P.; Dux, R.; Baak, M.; De Cola, L.; Balzani, V. Angew. Chem., Int. Ed. Engl. 1995, 34, 595-598.
31. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
32. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
33. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
34. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
35. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
36. Representative examples: Groshenny, V.; Harriman, A.; Ziessel, R. Angew. Chem., Int. Ed. Engl. 1995, 34, 1100-1102. Barigelletti, F.; Flamigni, L.; Guardigli, M.; Juris, A.; Beley, M.; Chodorowski-Kimmes, S.; Collin, J. P.; Sauvage, J. P. Inorg. Chem. 1996, 35, 136-142. Harriman, A.; Ziessel, R. Chem. Commun. 1996, 1707-1716. Ziessel, R.; Hissler, M.; El-ghayoury, A.; Harriman, A. Coord. Chem. Rev. 1998, 178-180, 1251-1298. Harriman, A.; Romero, F. M.; Ziessel, R. Benniston, A. C. J. Phys. Chem. A 1999, 103, 5399-5408. El-ghayoury, A.; Harriman, A.; Khatyr, A.; Ziessel, R. Angew. Chem., Int. Ed. 2000, 39, 185-189.
37. Mixed behavior, where both mechanisms are operative, has also been observed. See ref 5 and for example: Groshenny, V.; Harriman, A.; Hissler, M.; Ziessel, R. J. Chem. Soc., Faraday Trans. 1996, 92, 2223-2238.
38. Holmlin, R. E.; Tong, R. T.; Barton, J. K. J. Am. Chem. Soc. 1998, 120, 9724-9725.
39. Closs, G. L.; Miller, J. R. Science 1988, 240, 440-447. Closs, G. L.; Johnson, M. D.; Miller, J. R.; Piotrowiak, P. J. Am. Chem. Soc. 1989, 111, 3751-3753.
40. Closs, G. L.; Miller, J. R. Science 1988, 240, 440-447. Closs, G. L.; Johnson, M. D.; Miller, J. R.; Piotrowiak, P. J. Am. Chem. Soc. 1989, 111, 3751-3753.
41. Essentially an electron transfer phenomenon, the energy transfer rate is expected to decrease exponentially with increasing D/A separation . Thus, the following relationship should hold: k = A exp[-βR].
42. Turro, N. J. Modern Molecular Photochemistry: University Science Books: Sausalito, CA, 1991.
43. Hurley, D. J.; Tor. Y. J. Am. Chem. Soc. 1998, 120, 2194-2195.
44. Hurley, D. J.; Tor. Y. J. Am. Chem. Soc. 2002, 124, 3749-3762.
45. II excited state on the heterocycle-extended nucleoside (see ref 14).
46. II donor metal center (see ref 14).
47. II-modified oligonucleotides 6-11: calcd 6509.6 Da, found 6510 ± 6 Da.
48. II nucleosides.
49. II nucleoside (see also ref 14).
50. Distances were calculated using a helical model of the DNA duplex. See Supporting Information for details.
51. It is important to emphasize that the quenching observed is highly reproducible over several sample preparations and multiple measurements, suggesting minimal photodeterioration of the samples.
52. 2+ in Figure 5A.
53. Each measurement was corrected with respect to a control sample to which an equivalent amount of the nonmetalated complement had been added to correct for quenching that resulted simply from duplex formation (see also ref 14).
54. II luminescence at higher temperatures. See ref 3a.
55. II acceptor strand, indicating that under these conditions the potential sensitized emission is likely to be within the experimental error.
56. See Supporting Information for additional data.
57. 2.
58. This is a valid assumption when fluorophores are covalently linked to the DNA via long and flexible linkers.
59. II-containing duplexes are extremely low (∼0.006 for both the end- and internally modified duplexes), most likely because of the long lifetime of the Run chromophore relative to the tumbling rate of the oligonucleotides.
60. Note that saturating the linker also electronically "disconnects" the metal center and the nucleobase.
61. II-containing nucleoside 2 and its phosphoramidite.
62. II metal center in the metalated nucleoside rather than from the carbon analogous to the thymidine 5-methyl group because of the nearly symmetrical distribution of the excited over the diimine ligands (helical parameters a = 6, d = 11, L = 2 Å). See Supporting Information for details.
63. d = 0.042 vs 0.045, respectively).
64. 2+ (see Figure 5A).
65. The contribution of each decay is 50%, which is similar to the biexponential decay distributions observed in the single strands containing the conjugated nucleoside 1a.
66. This further supports that the 6% quenching observed at the largest D/A separation is interduplex static quenching (see ref 34 above).
67. 0 (see also ref 33 above).
68. See Supporting Information for an analysis of Barton's system (ref 9) according to the Förster energy transfer mechanism.
69. RuOs - 1) against distance, gives similar results.
70. Note that this is similar to the slope Barton obtained in analyzing the data reported in ref 9.
71. II dyads have been observed, See; Belser, P.; von Zelewsky, A.; Frank, M.; Seel, C.; Vögtle, F.; De Cola, L.; Barigelletti, F.; Balzani, V. J. Am. Chem. Soc. 1993, 115, 4076-4086.
72. It is interesting to add that Förster, in discussing transfer mechanisms for electronic excitation (ref 4a), demonstrates that in certain circumstances the curve for dipole-dipole energy transfer can be approximated by a simple exponential relationship.
73. Os(7) 12·7 shows no significant changes in steady-state luminescence quenching when compared to the case of the parent doubly modified duplex (see Supporting Information). These observations further suggest that nonradiative dipole-dipole interactions mediate energy transfer in these donor/ acceptor oligonucleotides.
74. Note we cannot unequivocally exclude minor contributions from redox-mediated quenching processes, although unpublished results from our lab show minimal strand or sequence dependence on D/A interactions in related oligonucleotides (to be published).