Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 32, 2008, Pages 11176-11181

  Iqbal, Asif ^a   Arslan, Sinan ^b   Okumus, Burak ^b   Wilson, Timothy J ^a   Giraud, Gerard ^d   Norman, David G ^a   Ha, Taekjip ^b,c   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b University of Illinois at Urbana Champaign   (United States)

^c UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^d UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

Cyanine fluorophores; FRET; Kappa squared; Single molecule FRET

Indexed keywords

DOUBLE STRANDED DNA;

ARTICLE; DNA HELIX; DNA HYBRIDIZATION; DNA STRUCTURE; ENERGY TRANSFER; FLUORESCENCE RESONANCE ENERGY TRANSFER; GEOMETRY; PRIORITY JOURNAL; RNA HYBRIDIZATION;

CARBOCYANINES; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, CHEMICAL; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HETERODUPLEXES;

EID: 48249085467     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0801707105     Document Type: Article

References (26)

1. Stryer L, Haugland RP (1967) Energy transfer: A spectroscopic ruler. Proc Natl Acad Sci USA 58:719-726.
2. Clegg RM (1996) Fluorescence Imaging Spectroscopy and Microscopy, eds Wang XF, Herman B (Wiley, New York), pp 179-252.
3. Lilley DMJ, Wilson TJ (2000) Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr Opin Chem Biol 4:507-517.
4. Clegg RM (2002) FRET tells us about proximities, distances, orientations and dynamic properties. J Biotechnol 82:177-179.
5. Haas E, Katchalski-Katzir E, Steinberg IZ (1978) Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization. Biochemistry 17:5064-5070.
6. Dale RE, Eisinger J, Blumberg WE (1979) The orientation freedom of molecular probes. The orientation factor in intramolecular energy transfer. Biophys J 26:161-194.
7. Wu P, Brand L (1992) Orientation factor in steady-state and time resolved resonance energy transfer measurements Biochemistry 31:7939-7947.
8. Unruh JR, Gokulrangan G, Lushington GH, Johnson CK, Wilson GS (2005) Orientational dynamics and dye-DNA interactions in a dye-labeled DNA aptamer. Biophys J 88:3455-3465.
9. VanBeek DB, Zwier MC, Shorb JM, Krueger BP (2007) Fretting about FRET: Correlation between kappa and R. Biophys J 92:4168-4178.
10. Lewis FD, Zhang L, Zuo X (2005) Orientation control of fluorescence resonance energy transfer using DNA as a helical scaffold. J Am Chem Soc 127:10002-10003.
11. Norman DG, Grainger RJ, Uhrin D, Lilley DMJ (2000) The location of Cyanine-3 on double-stranded DNA; importance for fluorescence resonance energy transfer studies Biochemistry 39:6317-6324.
12. Förster T (1948) Zwischenmolekulare Energiewanderung und Fluoreszenz Ann Phys 2:55-75.
13. Clegg RM (1992) Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol 211:353-388.
14. Clegg RM, Murchie AIH, Zechel A, Lilley DMJ (1993) Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc Natl Acad Sci USA 90:2994-2998.
15. Okumus B, Wilson TJ, Lilley DMJ, Ha T (2004) Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic Biophys J 87:2798-2806, .
16. Ha T, et al. (2002) Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase Nature 419:638-641, .
17. Sanborn ME, Connolly BK, Gurunathan K, Levitus M (2007) Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. J Phys Chem B 111:11064-11074.
18. Chibisov AK, et al. (1995) Photorelaxation processes in covalently linked indocarbocyanine and thiacarbocyanine dyes. J Phys Chem 99:886-893.
19. Horton NC, Finzel BC (1996) The structure of an RNA/DNA hybrid: a substrate of the ribonuclease activity of HIV-1 reverse transcriptase. J Mol Biol 264:521-533.
20. Xiong Y, Sundaralingam M (2000) Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucleic Acids Res 28:2171-2176.
21. Kopka ML, Lavelle L, Han GW, Ng HL, Dickerson RE (2003) An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H. J Mol Biol 334:653-665.
22. Beaucage SL, Caruthers MH (1981) Deoxynucleoside phosphoramidites - a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett 22:1859-1862.
23. Wilson TJ, Zhao Z-Y, Maxwell K, Kontogiannis L, Lilley DMJ (2001) Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme Biochemistry 40:2291-2302.
24. Boukobza E, Sonnenfeld A, Haran G (2001) Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy. J Phys Chem B 105:12165-12170.
25. Neely RK, Magennis SW, Dryden DTF, Jones AC (2004) Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements J Phys Chem B 108:17606 -17610.
26. Iqbal A, Wang L, Thompson KC, Lilley DMJ, Norman DG (2008) The structure of Cyanine 5 terminally attached to double-stranded DNA: Implication for FRET studies. Biochemistry, in press