Large-amplitude picosecond anisotropy decay of the intrinsic fluorescence of double-stranded DNA

Biophysical Journal

Volumn 70, Issue 4, 1996, Pages 1909-1922

  Georghiou, S ^a   Bradrick, Thomas D ^a   Philippetis, Alexander ^a   Beechem, Joseph M ^b  

^a UNIVERSITY OF TENNESSEE   (United States)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BASE; DOUBLE STRANDED DNA; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE); POLYTHYMIDYLIC ACID;

ANISOTROPY; ARTICLE; DEPOLARIZATION; DNA CONFORMATION; FLUORESCENCE; NUCLEOTIDE SEQUENCE;

EID: 0029958871     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(96)79755-2     Document Type: Article

References (105)

1. Alam, T. M., and G. P. Drobny 1991. Solid-state NMR studies of DNA structure and dynamics. Chem Rev. 91:1545-1590.
2. Allison, S. A., and J. M. Schurr. 1979. Torsion dynamics and depolarization of fluorescence of linear macromolecules. I. Theory and application to DNA. Chem. Phys. 41:35-59
3. Allison, S. A., J. H. Shibata, J. Wilcoxon, and J. M. Schurr. 1982. NMR relaxation of DNA. I. The contribution of torsional deformation modes of the elastic filament. Biopolymers. 21:729-762.
4. Aoki, T. I., and P. R. Callis. 1982. The fluorescence of native DNA at room temperature. Chem. Phys. Lett. 92:327-332.
5. Ballini, J. P., P. Vigny, and M. Daniels. 1983. Synchrotron excitation of DNA fluorescence: decay time evidence for excimer emission at room temperature. Biophys. Chem. 18:61-65.
6. Barber, E. J. 1966. Calculation of density and viscosity of sucrose solutions as a function of concentration and temperature. Natl. Cancer Inst. Monogr. 21:219-239.
7. Barcelo, F, G. Muzard, R. Mendoza, B. Revet, B. P. Roques, and J.-B. Le Pecq. 1991. Removal of DNA curving by DNA ligands: gel electrophoresis study. Biochemistry. 30:4863-4873.
8. Barkley, M. D., and B. H. Zimm. 1979. Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA. J. Chem. Phys. 70.2991-3007.
9. Becker, M., and Z. Wang. 1989. Origin of ultraviolet damage in DNA. J. Mol. Biol. 210:429-438.
10. Beechem, J. M., E. Gratton, M. Ameloot, J. R. Knutson, and L. Brand. 1991. The global analysis of fluorescence intensity and anisotropy decay data: second-generation theory and programs. In Topics in Fluorescence Spectroscopy, Vol. 2. J. R. Lakowicz, editor. Plenum, New York. 241-305.
11. Bendel, P., O. Laub, and T. L. James. 1982. Molecular motions of super-coiled and circular DNA. A phosphorus-31 nuclear magnetic resonance study. J. Am. Chem. Soc. 104:6748-6754.
12. Beveridge, D. L., and G. Ravishanker. 1994. Molecular dynamics studies of DNA. Curr. Opin. Struct. Biol. 4:246-255.
13. Birchall, A. J., and A. N. Lane. 1990. Anisotropic rotation in nucleic acid fragments: significance for determination of structures from NMR data. Eur. Biophys. J. 19:73-78.
14. Birks, J. B. 1970. Photophysics of Aromatic Molecules. John Wiley, New York.
15. 31P NMR. J. Am. Chem. Soc. 102:25-31.
16. 13C-NMR relaxation in three DNA oligonucleotide duplexes: model-free analysis of internal and overall motion. Biochemistry. 33:2441-2450.
17. 15). J. Biol. Chem. 250:5109-5113.
18. Cadet, J., and P. Vigny. 1990. The photochemistry of nucleic acids. In Bioorganic Photochemistry. Vol. 1. H. Morrison, editor. John Wiley, New York. 1-272.
19. Callis, P. R. 1979. Polarized fluorescence and estimated lifetimes of the DNA bases at room temperature. Chem. Phys. Lett. 61:563-567.
20. Callis, P. R. 1983. Electronic states and luminescence of nucleic acid systems. Annu. Rev. Phys. Chem. 34:329-357.
21. Cantor, C. R., and P. R. Schimmel. 1980. Biophysical Chemistry, Part II. W. H. Freeman and Co., New York.
22. Chou, K.-C., and B. Mao. 1988. Collective motion in DNA and its role in drug intercalation. Biopolymers. 27:1795-1815.
23. Chou, P.-J., and W. C. Johnson. 1993. Base inclinations in natural and synthetic DNAs. J. Am. Chem. Soc. 115:1205-1214.
24. Chuprina, V. P. 1987. Anomalous structure and properties of poly(dA)·poly(dT). Computer simulation of the polynucleotide structure with the spine of hydration in the minor groove Nucleic Acids Res. 15:293-311.
25. Coll, M., C. A. Frederick, A. H.-J Wang, and A. Rich. 1987. A bifurcated hydrogen-bonded conformation in the d(A-T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc Natl. Acad. Sci. USA. 84:8385-8389.
26. Daniels, M., L. P. Hart, P. S. Ho. J. P. Ballini, and P. Vigny. 1990. Time-resolved spectroscopy of the intrinsic fluorescence of nucleic acid species. Proc. SPIE. 1204:304-313.
27. Daniels, M., and W. W. Hauswirth. 1971. Fluorescence of the purine and pyrimidine bases of the nucleic acids in neutral solution at 300 K. Science. 171:675-677.
28. Daniels, M., C. S. Shaar, and J. P. Morgan. 1988. Sequence-dependent emission from stacked forms of ApC and CpA. Evidence for stacked base ("dimer") absorption and left-handed stacked conformation Biophys. Chem. 32:229-237.
29. Dexter, D. L. 1953. A theory of sensitized luminescence in solids. J. Chem. Phys. 21:836-850.
30. Dickerson, R. E., D. S. Goodsell, and S. Neidle. 1994. The tyranny of the lattice. Proc. Natl Acad. Sci. USA. 91:3579-3583.
31. Drew, H. R., and R. E. Dickerson. 1981. Structure of a B-DNA dodecamer III. Geometry of hydration. J. Mol. Biol. 151:535-556.
32. Edward, J. T. 1970. Molecular volumes and the Stokes-Einstein equation. J. Chem. Educ. 47:261-270.
33. Eimer, W., and R. Pecora. 1991. Rotational and translational diffusion of short rodlike molecules in solution: oligonucleotides. J. Chem. Phys. 94:2324-2329.
34. Eimer, W., J. R. Williamson, S. G Boxer, and R. Pecora. 1990. Characterization of the overall and internal dynamics of short oligonucleotides by depolarized dynamic light scattering and NMR relaxation measurements. Biochemistry. 29:799-811.
35. Förster, Th. 1965. Delocalization excitation and excitation transfer. In Modern Quantum Chemistry, Part III. O. Sinanoǧlu, editor. Academic Press, New York. 93-137.
36. Fritsch, V., G. Ravishanker, D. L. Beveridge, and E. Westhof. 1993. Molecular dynamics simulations of poly(dA)·poly(dT): comparisons between implicit and explicit solvent representations. Biopolymers. 33: 1537-1552.
37. Garcia de la Torre, J., S. Navarro, and M. C. L. Martinez. 1994. Hydrodynamic properties of a double-helical model for DNA. Biophys. J. 66:1573-1579.
38. Ge, G., and S. Georghiou. 1991a. Excited-state properties of the alternating polynucleotide poly(dA-dT)·poly(dA-dT). Photochem. Photobiol. 54: 301-305.
39. Ge, G., and S. Georghiou. 1991b. Room-temperature fluorescence properties of the polynucleotide poly(dA)·poly(dT). Photochem. Photobiol. 54:477-480.
40. Georghiou, S., T. M. Nordlund, and A. M. Saim. 1985. Picosecond fluorescence decay time measurements of nucleic acids at room temperature in aqueous solution. Photochem. Photobiol. 41:209-212.
41. Georghiou, S., G. R. Phillips, and G. Ge. 1992. Resolution of the electronic absorption spectra of the adenine and thymine residues in poly(dA)·poly(dT). Biopolymers. 32:1417-1420.
42. Georghiou, S., G. R. Phillips, L. S. Gerke, A. Philippetis, and T. D Bradrick. 1994. Photophysical properties of nucleic acids that contain A and T bases and global analysis of steady-state fluorescence spectra in the presence of energy transfer. Proc. SPIE. 2137:696-706.
43. Georghiou, S., S. Zhu, R. Weidner, C.-R. Huang, and G. Ge. 1990 Singlet-singlet energy transfer along the helix of a double-stranded nucleic acid at room temperature. J. Biomol. Struct. Dyn. 8:657-674.
44. Gueron, M., J. Eisinger, and A. A. Lamola. 1974. Excited states of nucleic acids. In Basic Principles of Nucleic Acid Chemistry. P. O. P. Ts'o. editor. Academic Press, New York. 311-398.
45. Guest, C. R., R. A. Hochstrasser, L. C. Sowers, and D. P. Millar. 1991 Dynamics of mismatched base pairs in DNA. Biochemistry. 30: 3271-3279.
46. Hard, T., and D. Kearns. 1986, Association of short DNA fragments: steady state fluorescence polarization study. Biopolymers. 25. 1519-1529.
47. Harrington, R. E., and I. Winicov. 1994. New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. Prog. Nucleic Acid. Res. Mol Biol. 47:195-270.
48. Hauswirth, W. W., and M. Daniels. 1976. Excited states of nucleic acids. polymeric forms. In Photochemistry and Photobiology of Nucleic Acids. S. Y Wang, editor. Academic Press, New York. 110-167.
49. Hogan, M. E., N. Dattagupta, and D. M. Crothers. 1978. Transient electric dichroism of rod-like DNA molecules. Proc. Natl. Acad. Sci. USA. 75:195-199.
50. Hogan, M. E., N. Dattagupta, and D. M. Crothers. 1979a. Transmission of allosteric effects in DNA. Nature. 278:521-524.
51. Hogan, M. E., N. Dattagupta, and D. M. Crothers. 1979b. Transient electric dichroism studies of the structure of the DNA complex with intercalated drugs. Biochemistry. 18:280-288.
52. Hogan, M. E., and O. Jardetzky. 1980. Internal motions in DNA. Proc. Natl. Acad Sci. USA. 76:6341-6345.
53. Holbrook, S. R., and S.-H. Kim. 1984. Local mobility of nucleic acids as determined from crystallographic data. J. Mol. Biol. 173:361-388.
54. Hustedt, E. J., A. Spaltenstein, J. J. Kirchner, P. B. Hopkins, and B. H. Robinson. 1993. Motions of short DNA duplexes: an analysis of DNA dynamics using an EPR-active probe. Biochemistry. 32:1774-1787.
55. Johnson, W. C., and I. Tinoco. 1969. Circular dichroism of polynucleotides: a simple theory. Biopolymers. 7:727-749.
56. Kollman, P. A., P. K. Weiner, and A. Dearing. 1981. Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers. Biopolymers. 20:2583-2621.
57. Lakowicz, J. R. 1983. Principles of Fluorescence Spectroscopy, Plenum, New York.
58. Lee, S. A., S. M. Lindsay, J. W. Powell, T. Weidlich, N. J. Tao, G. D. Lewen, and A. Rupprecht. 1987. A Bnllouin scattering study of the hydration of Li- and Na-DNA films. Biopolymers. 26:1637-1665.
59. Leroy, J. L., M. Kochoyan, T. Huynh-Dinh, and M. Guéron. 1988. Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of imino proton. J. Mol. Biol. 200:223-238.
60. Lozansky, E. D., H. M. Sobell, and M. Lessen. 1979. Does DNA have two structures that coexist at equilibrium? In Stereodynamics of Molecular Systems, R. H. Sarma, editor. Pergamon Press, New York. 265-271.
61. Ludescher, R. D., L. Peting, S. Hudson, and B. Hudson. 1987. Time-resolved fluorescence anisotropy for systems with lifetime and dynamic heterogeneity. Biophys. Chem. 28:59-75.
62. Magde, D., M. Zappala, W. H. Knox, and T. M Nordlund. 1983. Picosecond fluorescence anisotropy decay in the ethidium/DNA complexes. J. Phys. Chem. 87:3286-3288.
63. McConnell, K. J., R. Nirmala, M. A. Young, G. Ravishanker, and D. L. Beveridge. 1994. A nanosecond molecular dynamics trajectory for a B DNA double helix: evidence for substates. J. Am. Chem. Soc. 116: 4461-4462.
64. Miaskiewicz, K., R. Osman, and H. Weinstein. 1993. Molecular dynamics simulation of hydrated d(CGCGAATTCGCG), dodecamer. J. Am. Chem. Soc. 115:1526-1537.
65. Millar, D. P., R. J. Robbins, and A. H. Zewail. 1980. Direct observation of the torsional dynamics of DNA and RNA by picosecond Spectroscopy. Proc. Natl. Acad. Sci. USA. 77:5593-5597.
66. Millar, D. P., R. J. Robbins, and A. H. Zewail. 1982. Torsion and bending of nucleic acids studied by subnanosecond time-resolved fluorescence depolarization of intercalated dyes. J. Chem. Phys. 76:2080-2094.
67. Morgan, J. P., and M. Daniels. 1978. Intrinsic polarization and rotational depolarization of fluorescence of DNA bases in aqueous solution at room temperature. Photochem. Photobiol. 27:73-75.
68. Morgan, J. P., and M. Daniels. 1980a. Excited states of DNA and its components at room temperature. III. Spectra, polarization and quantum yields of emissions from ApA and poly rA. Photochem. Photobiol. 31:101-113.
69. Morgan, J. P., and M. Daniels. 1980b. Excited states of DNA and its components at room temperature. IV. Spectral, polarization and quantum yield studies of emissions from CpC and poly rC. Photochem. Photobiol. 31:207-213.
70. Nelson, H. C. M., J. T. Finch, B. F. Luisi, and A. Klug. 1987. The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature. 330:221-226.
71. Nordlund, T. M., S. Andersson, L. Nilsson, R. Rigler, A. Gräslund, and L. W. McLaughlin. 1989. Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI recognition sequence: fluorescence, molecular dynamics, and NMR studies. Biochemistry. 28:9095-9103.
72. Nuutero, S., B. S. Fujimoto, P. F. Flynn, R. R. Reid, N. S. Ribeiro, and J. M. Schurr. 1994. The amplitude of local angular motion of purines in DNA in solution. Biopolymers. 34:463-480.
73. Poncin, M., B. Hartmann, and R. Lavery. 1992. Conformational sub-states in B-DNA. J Mol. Biol. 226:775-794.
74. Prabhakaran, M., and S. C. Harvey. 1988. Molecular dynamics of structural transitions and intercalation in DNA Biopolymers. 27:1239-1248.
75. Prohofsky, E. W. 1986. Motional dynamics of the DNA double helix. In Biomolecular Stereodynamics IV. R. H. Sarma and M. H. Sarma, editors. Adenine, Guilderland, NY. 21-46.
76. Ptashne, M. 1986. Gene regulation by proteins acting nearby and at a distance. Nature. 322:697-701.
77. Puhl, H. L., S. R. Gudibande, and M. J. Behe. 1991. Poly[d(A·T)] and other synthetic polydeoxynucleotides containing oligoadenosine tracts form nucleosomes easily. J. Mol. Biol. 222:1149-1160.
78. Ramstein, J., and R. Lavery. 1988. Energetic coupling between DNA bending and base pair opening. Proc. Natl. Acad. Sci. USA. 85: 7231-7235.
79. Rhodes, W. 1961. Hypochromism and other spectral properties of helical polynucleotides J. Am. Chem. Soc. 83:3609-3617.
80. Rhodes, W., and M. Chase. 1967. Generalized susceptibility theory. I. Theories of hypochromism. Rev. Mod. Phys. 39:348-361.
81. Rigler, R., F. Claesens, and O. Kristeasen. 1985. Picosecond fluorescence spectroscopy in the analysis of structure and motion of biopolymers. Anal. Instrum. 14:525-546.
82. Sarai, A., J. Mazur, R. Nussinov, and R. L. Jemigan. 1989. Sequence dependence of DNA conformational flexibility. Biochemistry. 28: 7842-7849.
83. Satchwell, S. C., H. R. Drew, and A. A. Travers. 1986. Sequence periodicities in nucleosome core DNA. J. Mol. Biol. 191:659-675.
84. Schleif, R. 1988. DNA looping. Science. 240:127-128.
85. Schurr, J. M., and B. S. Fujimoto. 1988. The amplitude of local angular motions of intercalated dyes and bases in DNA. Biopolymers. 27: 1543-1569.
86. Schurr, J. M., B. S. Fujimoto, P. Wu, and L. Song. 1991. Fluorescence studies of nucleic acids: dynamics, rigidities, and structures. In Topics in Fluorescence Spectroscopy, Vol. 3. J. R. Lakowicz, editor. Plenum, New York. 137-229.
87. Simpson, W. T., and D. L. Peterson. 1957. Coupling strength for resonance force transfer of electronic energy in van der Waals solids. J. Chem. Phys. 26:588-593.
88. Sobell, H. M., C. C. Tsai, S. C. Jain, and S. G. Gilbert. 1977. Visualization of drug-nucleic acid interactions at atomic resolution III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions. J. Mol. Biol. 114:333-365.
89. Srinivasan, A. R., and W. K. Olson. 1987. Nucleic acid model building: the multiple backbone solutions associated with a given base morphology. J. Biomol Struct. Dyn. 4:895-938.
90. Sullivan, K. M., A. I. H. Murchie, and D. M. J. Lilley. 1988. Long range structural communication between sequences in supercoiled DNA. Sequence dependence of contextual influence on cruciform extrusion mechanism. J. Biol. Chem. 263:13074-13082.
91. Swaminathan, S., G. Ravishanker, and D. L. Beveridge. 1991. Molecular dynamics of B-DNA including water and counterions: a 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field. J. Am. Chem. Soc. 113:5027-5040.
92. Théveny, B., D. Coulaud, M. Le Bret, and B. Révet. 1988. Local variations of curvature and flexibility along DNA molecules analyzed from electron micrographs. In Structure and Expression. Vol. 3. W. K. Olson, M. H. Sarma, R. H. Samoa, and M. Sundaralingam, editors. Adenine Press, Guilderiand, NY. 39-55.
93. Thomas, J. C., S A. Allison, C. J. Appellof, and J. M. Schurr. 1980. Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral Φ29 DNA. Biophys. Chem. 12:177-188.
94. Tinoco, I. 1960. Hypochromism in polynucleotides. J. Am. Chem. Soc. 82:4785-4790.
95. Tinoco, I. 1961. Erratum: optical and other electronic properties of polymers. J. Am. Chem. Soc. 84:1067.
96. Tirado, M. M., and J. Garcia de la Torre. 1980. Rotational dynamics of rigid, symmetric top macromolecules. Application to circular cylinders. J. Chem. Phys. 73:1986-1993.
97. Vigny, P., and J. P. Ballini. 1977. Excited states of nucleic acids at 300 K and electronic energy transfer. In Excited States in Organic Chemistry and Biochemistry. B. Pullman and N. Goldblum, editors. D. R. Reidel, Boston. 1-13.
98. Vigny, P., and M. Duquesne. 1976. On the fluorescence properties of nucleotides and polynucleotides at room temperature. In Excited States of Biological Molecules. J. B. Birks, editor. John Wiley, New York. 167-177.
99. Voet, D., W. B. Gratzer, R. A. Cox. and P. Doty. 1963. Absorption spectra of nucleotides, polynucleotides, and nucleic acids in the far ultraviolet. Biopolymers. 1:193-208.
100. Wahl, Ph., J. Paoletti, and J.-B. Le Pecq. 1970. Decay of fluorescence emission anisorropy of the ethidium bromide-DNA complex evidence for an internal motion in DNA. Proc. Natl. Acad. Sci. USA. 65:417-421.
101. Watson, J. D., N. H. Hopkins, J W Roberts, J. A. Steitz, and A. M. Weiner. 1987. Molecular Biology of the Gene, 4th Ed. Benjamin/Cummings, Menlo Park, CA.
102. Weber, G., and M. Shinitzky. 1970. Failure of energy transfer between identical aromatic molecules on excitation at the long wave edge of the absorption spectrum. Proc. Natl. Acad. Sci. USA. 65:823-830.
103. Williams, S. A., C. N. Renn, and P. R. Callis. 1987. Polarized fluorescence of thymine in neutral aqueous solution at room temperature: evidence for interference from the anion and for the ππ* nature of the fluorescence. J. Phys. Chem. 91:2730-2734.
104. Wilson, R. W., and P. R. Callis. 1976. Excitons, energy transfer, and charge resonance in excited dinucleotides and polynucleotides. A photoselection study. J. Phys. Chem. 80:2280-2288.
105. Zakrweska, K. 1992. Static and dynamic conformational properties of AT sequences in B-DNA. J. Biomol Struct. Dyn. 9:681-693.