Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences

Photochemical and Photobiological Sciences

Volumn 5, Issue 5, 2006, Pages 493-498

  Jockusch, Steffen ^a   Martí, Angel A ^a   Turro, Nicholas J ^a   Li, Zengmin ^a,b   Li, Xiaoxu ^b   Ju, Jingyue ^a,b   Stevens, Nathan ^c   Akins, Daniel L ^c  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b Columbia University College of Physicians and Surgeons ^*  (United States)

^c CITY COLLEGE OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE;

ANALYTIC METHOD; ARTICLE; DNA PROBE; DNA SEQUENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE TARGETING; MEASUREMENT; PRIORITY JOURNAL; RNA PROBE; RNA SEQUENCE; SENSOR; SEQUENCE ANALYSIS; SPECTROSCOPY;

ALEXA;

EID: 33646587015     PISSN: 1474905X     EISSN: 14749092     Source Type: Journal    
DOI: 10.1039/b600213g     Document Type: Article

References (25)

1. W. Tan X. Fang J. Li X. Liu Molecular beacons: a novel DNA probe for nucleic acid and protein studies Chem.–Eur. J. 2000 6 1107-1111.
2. T. Antony V. Subramaniam Molecular Beacons: Nucleic Acid Hybridization and Emerging Applications J. Biomol. Struct. Dyn. 2001 19 4997-5004.
3. G. Bonnet S. Tyagi A. Libchaber F. R. Kramer Thermodynamic basis of the enhanced specificity of structured DNA probes Proc. Natl. Acad. Sci. U. S. A. 1999 96 6171-6176.
4. S. Tyagi F. R. Kramer Molecular Beacons: Probes that Fluoresce upon Hybridization Nat. Biotechnol. 1996 14 303-308.
5. S. Tyagi D. P. Bratu F. R. Kramer Multicolor molecular beacons for allele discrimination Nat. Biotechnol. 1998 16 49-58.
6. K. Faulds L. Fruk D. C. Robson D. G. Thompson A. Enright W. E. Smith D. Graham A new approach for DNA detection by SERRS Faraday Discuss. 2006 10.1039/b506219e.
7. G. Bonnet O. Krichevsky A. Libchaber Kinetics of conformational fluctuations in DNA hairpin-loops Proc. Natl. Acad. Sci. U. S. A. 1998 95 8602-8606.
8. S. A. E. Marras F. R. Kramer S. Tyagi Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes Nucleic Acids Res. 2002 30 e122.
9. P. Zhang T. Beck W. Tan Design of a Molecular Beacon DNA Probe with Two Fluorophores Angew. Chem., Int. Ed. 2001 40 402-405.
10. A. A. Martí S. Jockusch Z. Li J. Ju N. J. Turro Molecular Beacons with intrinsically fluorescent nucleotides Nucleic Acids Res. 2006, accepted 10.1093/nar/gkl134.
11. K. Fujimoto H. Shimizu M. Inouye Unambiguous Detection of Target DNAs by Excimer-Monomer Switching Molecular Beacons J. Org. Chem. 2004 69 3271-3275.
12. C. J. Yang S. Jockusch M. Vincens N. J. Turro W. Tan Light-switching excimer probes for rapid protein monitoring in complex biological fluids Proc. Natl. Acad. Sci. U. S. A. 2005 102 17278-17283.
13. S. A. E. Marras, F. R. Kramer and S. Tyagi, Genotyping single nucleotide polymorphisms with molecular beacons, The Humana Press Inc., Towada, NJ, 2003, vol. 212, pp. 111–128.
14. J.-F. Brunet E. Shapiro S. A. Foster E. R. Kandel Y. Iino Identification of a peptide specific for Aplysia sensory neurons by PCR-based differential screening Science 1991 252 856-859.
15. N. Panchuk-Voloshina R. P. Haugland J. Bishop-Stewart M. K. Bhalgat P. J. Millard F. Mao W.-Y. Leung R. P. Haugland Alexa dyes, a series of new fluorescent dyes that yield exceptionally bright, photostable conjugates J. Histochem. Cytochem. 1999 47 1179-1188.
16. A. M. Iribarren B. S. Sproat P. Neuner I. Sulston U. Ryder A. I. Lamond 2′-O-alkyl oligoribonucleotides as antisense probes Proc. Natl. Acad. Sci. U. S. A. 1990 87 7747-7751.
17. P. Bratu Diana B.-J. Cha M. Mhlanga Musa R. Kramer Fred S. Tyagi Visualizing the distribution and transport of mRNAs in living cells Proc. Natl. Acad. Sci. U. S. A. 2003 100 13308-13313.
18. A. I. Lamond B. S. Sproat Antisense oligonucleotide made of 2′-O-AlkylRNA: their properties and applications in RNA biochemistry FEBS Lett. 1993 1–2 123-127.
19. T. Heinlein J.-P. Knemeyer O. Piestert M. Sauer Photoinduced Electron Transfer between Fluorescent Dyes and Guanosine Residues in DNA-Hairpins J. Phys. Chem. B 2003 107 7957-7964.
20. K. Stoer B. Haefner O. Nolte J. Wolfrum M. Sauer D.-P. Herten Species-Specific Identification of Mycobacterial 16S rRNAS PCR Amplificons Using Smart Probes Anal. Chem. 2005 77 7195-7203.
21. I. Nazarenko R. Pires B. Lowe M. Obaidy A. Rashtchian Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes Nucleic Acids Res. 2002 30 2089-2195.
22. E. Rusinova V. Tretyachenko-Ladokhina O. E. Vele D. F. Senear J. B. A. Ross Alexa and Oregon Green dyes as fluorescence anisotropy probes for measuring protein–protein and protein–nucleic acid interactions Anal. Biochem. 2002 308 18-25.
23. R. A. Hochstrasser S.-M. Chen D. P. Millar Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer Biophys. Chem. 1992 45 133-141.
24. J. R. Lakowicz, Topics in Fluorescence Spectroscopy, Volume 5: Nonlinear and Two-Photon-Induced Fluorescence, Plenum Press, New York, 1997, vol. 5, 544 pp.
25. A. Tsourkas M. A. Behlke Y. Xu G. Bao Spectroscopic features of dual fluorescence/luminescence resonance energy-transfer molecular beacons Anal. Chem. 2003 75 3697-3703.