Photophysical and dynamical properties of doubly linked Cy3-DNA constructs

Journal of Physical Chemistry B

Volumn 118, Issue 1, 2014, Pages 152-163

  Stennett, Elana M S ^a   Ma, Ning ^b   Van Der Vaart, Arjan ^b   Levitus, Marcia ^a  

^a Arizona State University   (United States)

^b UNIVERSITY OF SOUTH FLORIDA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE SPECTROSCOPY; ISOMERIZATION; ISOMERS; MOLECULAR DYNAMICS;

DYNAMICAL PROPERTIES; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE QUANTUM YIELD; FREE ENERGY SIMULATIONS; MOLECULAR DYNAMICS SIMULATIONS; PHOTOPHYSICAL MEASUREMENTS; TIME-RESOLVED FLUORESCENCE; TRANSIENT ABSORPTION;

DNA;

CARBOCYANINE; CYANINE DYE 3; DNA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS; PHOTOCHEMISTRY; SPECTROFLUOROMETRY;

CARBOCYANINES; DNA; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; PHOTOCHEMICAL PROCESSES; SPECTROMETRY, FLUORESCENCE;

EID: 84892600013     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp410976p     Document Type: Article

References (66)

1. Lilley, D. M. J.; Wilson, T. J. Fluorescence Resonance Energy Transfer as a Structural Tool for Nucleic Acids Curr. Opin Chem. Biol. 2000, 4 (5) 507-517
2. Michalet, X.; Weiss, S.; Jager, M. Single-Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics Chem. Rev. 2006, 106 (5) 1785-1813
3. Royer, C. A. Probing Protein Folding and Conformational Transitions with Fluorescence Chem. Rev. 2006, 106 (5) 1769-1784
4. Borgia, A.; Williams, P. M.; Clarke, J. Single-Molecule Studies of Protein Folding Annu. Rev. Biochem. 2008, 77, 101-125
5. Park, H.; Toprak, E.; Selvin, P. R. Single-Molecule Fluorescence to Study Molecular Motors Q. Rev. Biophys. 2007, 40 (1) 87-111
6. Cordes, T.; Maiser, A.; Steinhauer, C.; Schermelleh, L.; Tinnefeld, P. Mechanisms and Advancement of Antifading Agents for Fluorescence Microscopy and Single-Molecule Spectroscopy Phys. Chem. Chem. Phys. 2011, 13 (14) 6699-6709
7. Rasnik, I.; McKinney, S. A.; Ha, T. Nonblinking and Longlasting Single-Molecule Fluorescence Imaging Nat. Methods 2006, 3 (11) 891-893
8. Gopich, I. V.; Szabo, A. Theory of the Energy Transfer Efficiency and Fluorescence Lifetime Distribution in Single-Molecule FRET Proc. Natl. Acad. Sci. U. S. A. 2012, 109 (20) 7747-7752
9. McKinney, S. A.; Joo, C.; Ha, T. Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling Biophys. J. 2006, 91 (5) 1941-1951
10. Taylor, J. N.; Makarov, D. E.; Landes, C. F. Denoising Single-Molecule FRET Trajectories with Wavelets and Bayesian Inference Biophys. J. 2010, 98 (1) 164-173
11. Watkins, L. P.; Yang, H. Information Bounds and Optimal Analysis of Dynamic Single Molecule Measurements Biophys. J. 2004, 86 (6) 4015-4029
12. Milas, P.; Gamari, B. D.; Parrot, L.; Krueger, B. P.; Rahmanseresht, S.; Moore, J.; Goldner, L. S. Indocyanine Dyes Approach Free Rotation at the 3′ Terminus of A-RNA: A Comparison with the 5′ Terminus and Consequences for Fluorescence Resonance Energy Transfer J. Phys. Chem. B 2013, 117 (29) 8649-8658
13. Spiriti, J.; Binder, J. K.; Levitus, M.; van der Vaart, A. Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair Biophys. J. 2011, 100 (4) 1049-1057
14. Norman, D. G.; Grainger, R. J.; Uhrin, D.; Lilley, D. M. J. Location of Cyanine-3 on Double-Stranded DNA: Importance for Fluorescence Resonance Energy Transfer Studies Biochemistry 2000, 39 (21) 6317-6324
15. Urnavicius, L.; McPhee, S. A.; Lilley, D. M. J.; Norman, D. G. The Structure of Sulfoindocarbocyanine 3 Terminally Attached to dsDNA via a Long, Flexible Tether Biophys. J. 2012, 102 (3) 561-568
16. Ranjit, S.; Gurunathan, K.; Levitus, M. Photophysics of Backbone Fluorescent DNA Modifications: Reducing Uncertainties in FRET J. Phys. Chem. B 2009, 113 (22) 7861-7866
17. Ranjit, S.; Levitus, M. Probing the Interaction Between Fluorophores and DNA Nucleotides by Fluorescence Correlation Spectroscopy and Fluorescence Quenching Photochem. Photobiol. 2012, 88 (4) 782-791
18. Harvey, B. J.; Perez, C.; Levitus, M. DNA Sequence-Dependent Enhancement of Cy3 Fluorescence Photochem. Photobiol. Sci. 2009, 8 (8) 1105-1110
19. Sanborn, M. E.; Connolly, B. K.; Gurunathan, K.; Levitus, M. Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA J. Phys. Chem. B 2007, 111 (37) 11064-11074
20. Harvey, B. J.; Levitus, M. Nucleobase-Specific Enhancement of Cy3 Fluorescence J. Fluoresc. 2009, 19 (3) 443-448
21. Neubauer, H.; Gaiko, N.; Berger, S.; Schaffer, J.; Eggeling, C.; Tuma, J.; Verdier, L.; Seidel, C. A. M.; Griesinger, C.; Volkmer, A. Orientational and Dynamical Heterogeneity of Rhodamine 6G Terminally Attached to a DNA Helix Revealed by NMR and Single-Molecule Fluorescence Spectroscopy J. Am. Chem. Soc. 2007, 129 (42) 12746-12755
22. Vamosi, G.; Gohlke, C.; Clegg, R. M. Fluorescence Characteristics of 5-Carboxytetramethylrhodamine Linked Covalently to the 5′ End of Oligonucleotides: Multiple Conformers of Single-Stranded and Double-Stranded Dye-DNA Complexes Biophys. J. 1996, 71 (2) 972-994
23. Majumdar, Z. K.; Hickerson, R.; Noller, H. F.; Clegg, R. M. Measurements of Internal Distance Changes of the 30 S Ribosome Using FRET with Multiple Donor-Acceptor Pairs: Quantitative spectroscopic methods J. Mol. Biol. 2005, 351 (5) 1123-1145
24. Iqbal, A.; Arslan, S.; Okumus, B.; Wilson, T. J.; Giraud, G.; Norman, D. G.; Ha, T.; Lilley, D. M. J. Orientation Dependence in Fluorescent Energy Transfer Between Cy3 and Cy5 Terminally Attached to Double-Stranded Nuclelic Acids Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (32) 11176-11181
25. Dale, R. E.; Eisinger, J.; Blumberg, W. E. Orientational Freedom of Molecular Probes-Orientation Factor in Intra-Molecular Energy-Transfer Biophys. J. 1979, 26 (2) 161-193
26. Magde, D.; Brannon, J. H.; Cremers, T. L.; Olmsted, J. Absolute Luminescence Yield of Cresyl Violet-Standard for the Red J. Phys. Chem. 1979, 83 (6) 696-699
27. 2+ ChemPhysChem 2012, 13 (4) 909-913
28. Ciuba, M. A.; Levitus, M. Manganese-Induced Triplet Blinking and Photobleaching of Single Molecule Cyanine Dyes ChemPhysChem 2013, 14 (15) 3495-502
29. Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures Nucleic Acids Res. 2003, 31, 5108-5121
30. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79 (2) 926-35
31. Ferrenberg, A. M.; Swendsen, R. H. Optimized Monte Carlo Data Analysis Phys. Rev. Lett. 1989, 63 (12) 1195-8
32. Brooks, B. R.; Brooks, C. L., III; MacKerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30 (10) 1545-1614
33. Hoover, W. G. Canonical Dynamics: Equilibrium Phase-Space Distributions Phys. Rev. A 1985, 31, 1695-1697
34. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes J. Comput. Phys. 1977, 23 (3) 327-341
35. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98 (12) 10089-10092
36. Hart, K.; Foloppe, N.; Baker, C. M.; Denning, E. J.; Nilsson, L.; MacKerell, A. D. Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium J. Chem. Theory Comput. 2012, 8 (1) 348-362
37. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics J. Mol. Graphics 1996, 14 (1) 33.
38. Cooper, M.; Ebner, A.; Briggs, M.; Burrows, M.; Gardner, N.; Richardson, R.; West, R. Cy3B (TM): Improving the Performance of Cyanine Dyes J. Fluoresc. 2004, 14 (2) 145-150
39. Rulliere, C. Laser Action and Photoisomerization of 3,3′-Diethyl Oxadicarbocyanine Iodide (DODCI)-Influence of Temperature and Concentration Chem. Phys. Lett. 1976, 43 (2) 303-308
40. Levitus, M.; Ranjit, S. Cyanine Dyes in Biophysical Research: The Photophysics of Polymethine Fluorescent Dyes in Biomolecular Environments Q. Rev. Biophys. 2011, 44 (1) 123-151
41. Mishra, A.; Behera, R. K.; Behera, P. K.; Mishra, B. K.; Behera, G. B. Cyanines During the 1990s: A Review Chem. Rev. 2000, 100 (6) 1973-2012
42. Sundstrom, V.; Gillbro, T. Viscosity-Dependent Isomerization Yields of Some Cyanine Dyes-a Picosecond Laser Spectroscopy Study J. Phys. Chem. 1982, 86 (10) 1788-1794
43. Korppitommola, J. E. I.; Hakkarainen, A.; Hukka, T.; Subbi, J. An Isomerization Reaction of a Cyanine Dye in Normal-Alcohols-Microscopic Friction and an Excited-State Barrier Crossing J. Phys. Chem. 1991, 95 (22) 8482-8491
44. Aramendia, P. F.; Negri, R. M.; Sanroman, E. Temperature-Dependence of Fluorescence and Photoisomerization in Symmetrical Carbocyanines-Influence of Medium Viscosity and Molecular-Structure J. Phys. Chem. 1994, 98 (12) 3165-3173
45. Gruber, H. J.; Hahn, C. D.; Kada, G.; Riener, C. K.; Harms, G. S.; Ahrer, W.; Dax, T. G.; Knaus, H. G. Anomalous Fluorescence Enhancement of Cy3 and Cy3.5 Versus Anomalous Fluorescence Loss of Cy5 and Cy7 upon Covalent Linking to IgG and Noncovalent Binding to Avidin Bioconjugate Chem. 2000, 11 (5) 696-704
46. Luschtinetz, F.; Dosche, C.; Kumke, M. U. Influence of Streptavidin on the Absorption and Fluorescence Properties of Cyanine Dyes Bioconjugate Chem. 2009, 20 (3) 576-582
47. Hwang, H.; Kim, H.; Myong, S. Protein Induced Fluorescence Enhancement as a Single Molecule Assay with Short Distance Sensitivity Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (18) 7414-7418
48. Sabanayagam, C. R.; Eid, J. S.; Meller, A., Using Fluorescence Resonance Energy Transfer to Measure Distances Along Individual DNA Molecules: Corrections due to Nonideal Transfer. J. Chem. Phys. 2005, 122 (6).
49. Chibisov, A. K.; Zakharova, G. V.; Gorner, H.; Sogulyaev, Y. A.; Mushkalo, I. L.; Tolmachev, A. I. Photorelaxation Processes in Covalently-Linked Indocarbocyanine and Thiacarbocyanine Dyes J. Phys. Chem. 1995, 99 (3) 886-893
50. Jia, K.; Wan, Y.; Xia, A. D.; Li, S. Y.; Gong, F. B.; Yang, G. Q. Characterization of Photoinduced Isomerization and Intersystem Crossing of the Cyanine Dye Cy3 J. Phys. Chem. A 2007, 111 (9) 1593-1597
51. Mcglynn, S. P.; Daigre, J.; Smith, F. J., External Heavy-Atom Spin-Orbital Coupling Effect. 4. Intersystem Crossing. J. Chem. Phys. 1963, 39 (3), 675.
52. Akesson, E.; Sundstrom, V.; Gillbro, T. Isomerization Dynamics in Solution Described by Kramers Theory with a Solvent-Dependent Activation-Energy Chem. Phys. 1986, 106 (2) 269-280
53. Elson, E. L.; Magde, D. Fluorescence Correlation Spectroscopy. 1. Conceptual Basis and Theory Biopolymers 1974, 13 (1) 1-27
54. Thompson, N. L., FLuorescence Correlation Spectroscopy. In Topics in Fluorescence Spectroscopy; Lakowicz, J. R., Ed.; Plenum Press: New York, 1991; Vol. 1, pp 337-355.
55. Digman, M. A.; Gratton, E. Fluorescence Correlation Spectroscopy and Fluorescence Cross-Correlation Spectroscopy Wires Syst. Biol. Med. 2009, 1 (2) 273-282
56. Krichevsky, O.; Bonnet, G. Fluorescence Correlation Spectroscopy: The Technique and Its Applications Rep. Prog. Phys. 2002, 65 (2) 251-297
57. Widengren, J.; Schwille, P. Characterization of Photoinduced Isomerization and Back-Isomerization of the Cyanine Dye Cy5 by Fluorescence Correlation Spectroscopy J. Phys. Chem. A 2000, 104 (27) 6416-6428
58. Enderlein, J.; I, G.; Patra, D.; Fitter, J. Art and Artefacts of Fluorescence Correlation Spectroscopy Curr. Pharm. Biotechnol. 2004, 5 (2) 155-161
59. Davis, L. M.; Shen, G. Q. Accounting for Triplet and Saturation Effects in FCS Measurements Curr. Pharm. Biotechnol. 2006, 7 (4) 287-301
60. Caselli, M.; Momicchioli, F.; Ponterini, G. Modeling of the Cis-Trans Partitioning in the Photoisomerizations of Cyanines and Stilbene Derivatives Chem. Phys. Lett. 1993, 216 (1-2) 41-46
61. Ponterini, G.; Momicchioli, F. Trans Cis Photoisomerization Mechanism of Carbocyanines-Experimental Check of Theoretical-Models Chem. Phys. 1991, 151 (1) 111-126
62. Tatikolov, A. S.; Akimkin, T. M.; Pronkin, P. G.; Yarmoluk, S. M. Enhancement of Photoisomerization of Polymethine Dyes in Complexes with Biomacromolecules Chem. Phys. Lett. 2013, 556, 287-291
63. Khimenko, V.; Chibisov, A. K.; Gorner, H. Effects of Alkyl Substituents in the Polymethine Chain on the Photoprocesses in Thiacarbocyanine Dyes J. Phys. Chem. A 1997, 101 (39) 7304-7310
64. Liu, R. S. H.; Asato, A. E. Photochemistry of Polyenes. 22. The Primary Process of Vision and the Structure of Bathorhodopsin-a Mechanism for Photoisomerization of Polyenes Proc. Natl. Acad. Sci. U. S. A. 1985, 82 (2) 259-263
65. Liu, R. S. H.; Hammond, G. S. Examples of Hula-Twist in Photochemical Cis-Trans Isomerization Chem.-Eur. J. 2001, 7 (21) 4536-4544
66. Liu, R. S. H. Photoisomerization by Hula-Twist. Photoactive Biopigments Pure Appl. Chem. 2002, 74 (8) 1391-1396