Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers

Biophysical Journal

Volumn 101, Issue 5, 2011, Pages 1148-1154

  Ouellet, Jonathan ^a   Schorr, Stephanie ^a   Iqbal, Asif ^a   Wilson, Timothy J ^a   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOCYANINE; CYANINE DYE 3; CYANINE DYE 5; DNA; FLUORESCENT DYE;

ARTICLE; BASE PAIRING; CHEMICAL STRUCTURE; CHEMISTRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; METABOLISM;

BASE PAIRING; CARBOCYANINES; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; MODELS, MOLECULAR;

EID: 80052463185     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.07.007     Document Type: Article

References (24)

1. L. Stryer, and R.P. Haugland Energy transfer: a spectroscopic ruler Proc. Natl. Acad. Sci. USA 58 1967 719 726
2. R.M. Clegg X.F. Wang, B. Herman, Fluorescence Imaging Spectroscopy and Microscopy 1996 John Wiley & Sons New York 179 252
3. D.M.J. Lilley, and T.J. Wilson Fluorescence resonance energy transfer as a structural tool for nucleic acids Curr. Opin. Chem. Biol. 4 2000 507 517
4. R.M. Clegg FRET tells us about proximities, distances, orientations and dynamic properties J. Biotechnol. 82 2002 177 179 (Pubitemid 34179599)
5. D.M.J. Lilley The structure and folding of branched RNA analyzed by fluorescence resonance energy transfer Methods Enzymol. 469 2009 159 187
6. C. Joo, and H. Balci T. Ha Advances in single-molecule fluorescence methods for molecular biology Annu. Rev. Biochem. 77 2008 51 76
7. T. Förster Intermolecular energy transfer and fluorescence [Zwischenmolekulare energiewanderung und fluoreszenz] Ann. Phys. 2 1948 55 75
8. E. Haas, E. Katchalski-Katzir, and I.Z. Steinberg Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization Biochemistry 17 1978 5064 5070
9. R.E. Dale, J. Eisinger, and W.E. Blumberg The orientational freedom of molecular probes. The orientation factor in intramolecular energy transfer Biophys. J. 26 1979 161 193
10. P. Wu, and L. Brand Orientation factor in steady-state and time-resolved resonance energy transfer measurements Biochemistry 31 1992 7939 7947
11. F.D. Lewis, L. Zhang, and X. Zuo Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold J. Am. Chem. Soc. 127 2005 10002 10003 (Pubitemid 40995436)
12. A. Iqbal, and S. Arslan D.M. Lilley Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids Proc. Natl. Acad. Sci. USA 105 2008 11176 11181
13. K. Börjesson, and S. Preus L.M. Wilhelmsson Nucleic acid base analog FRET-pair facilitating detailed structural measurements in nucleic acid containing systems J. Am. Chem. Soc. 131 2009 4288 4293
14. M. Levitus, and S. Ranjit Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments Q. Rev. Biophys. 44 2011 123 151
15. D.G. Norman, and R.J. Grainger D.M. Lilley Location of cyanine-3 on double-stranded DNA: importance for fluorescence resonance energy transfer studies Biochemistry 39 2000 6317 6324 (Pubitemid 30347135)
16. A. Iqbal, and L. Wang D.G. Norman The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies Biochemistry 47 2008 7857 7862
17. B.J. Harvey, and M. Levitus Nucleobase-specific enhancement of Cy3 fluorescence J. Fluoresc. 19 2009 443 448
18. E. Boukobza, A. Sonnenfeld, and G. Haran Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy J. Phys. Chem. B 105 2001 12165 12170 (Pubitemid 35338375)
19. B. Okumus, and T.J. Wilson T. Ha Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic Biophys. J. 87 2004 2798 2806
20. T. Ha Single-molecule fluorescence resonance energy transfer Methods 25 2001 78 86 (Pubitemid 32905290)
21. A.K. Chibisov, and G.V. Zakharova A.I. Tolmachev Photorelaxation processes in covalently linked indocarbocyanine and thiacarbocyanine dyes J. Phys. Chem. 99 1995 886 893
22. M.E. Sanborn, and B.K. Connolly M. Levitus Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA J. Phys. Chem. B 111 2007 11064 11074 (Pubitemid 47522599)
23. J. Spiriti, and J.K. Binder A. van der Vaart Cy3-DNA stacking interactions strongly depend on the identity of the terminal basepair Biophys. J. 100 2011 1049 1057
24. S. Ranjit, K. Gurunathan, and M. Levitus Photophysics of backbone fluorescent DNA modifications: reducing uncertainties in FRET J. Phys. Chem. B 113 2009 7861 7866