Synthesis of hairpin probe using deoxyguanosine as a quencher: Fluorescence and hybridization studies

Analytical Biochemistry

Volumn 364, Issue 1, 2007, Pages 86-88

  Misra, Arvind ^a,b   Kumar, P ^a,b   Gupta, K C ^a,b  

^a BANARAS HINDU UNIVERSITY   (India)

^b CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY;

CHEMISTRY;

DEOXYGUANOSINE;

5' UNTRANSLATED REGION; ARTICLE; CONFORMATIONAL TRANSITION; DNA HYBRIDIZATION; DNA PROBE; FAST PROTEIN LIQUID CHROMATOGRAPHY; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYDROPHOBICITY; MOLECULAR INTERACTION; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; SYNTHESIS;

EID: 33947625518     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2007.02.003     Document Type: Article

References (23)

1. Tyagi S., and Kramer F.R. Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol. 14 (1996) 303-308
2. Walter N.G., and Bruke J.M. Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. RNA 3 (1997) 392-404
3. Knemeyer J.P., Marme N., and Sauer M. Probes for detection of specific DNA sequences at the single-molecule level. Anal. Chem. 72 (2000) 3717-3724
4. Dubertret B., Calame M., and Libchaber A.J. Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat. Biotechnol. 19 (2001) 365-370
5. Johansson M.K., Fidder H., Dick D., and Cook R.M. Intramolecular dimers: A new strategy to fluorescence quenching in dual-labeled oligonucleotide probes. J. Am. Chem. Soc. 124 (2002) 6950-6956
6. Seidel C.A.M., Schulz A., and Sauer M. Nucleobase specific quenching of fluorescent dyes: I. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J. Phys. Chem. 100 (1996) 5541-5553
7. Crockett A.O., and Wittwer C.T. Fluorescein-labeled oligonucleotides for real-time PCR using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem. 290 (2001) 89-97
8. Sauer M. Single-molecule-sensitive fluorescent sensors based on photoinduced intramolecular charge transfer. Angew. Chem. Intl. Ed. 42 (2003) 1790-1793
9. Eggeling C., Fries J.R., Brand L., Gunther R., and Seidel C.A.M. Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy. Proc. Natl. Acad. Sci. USA 95 (1998) 1556-1561
10. Widengren J., Dapprich J., and Rigler R. Charge-transfer and stacking reactions between Rh6G and dGTP in water: A fluorescence correlation spectroscopy study. Chem. Phys. 216 (1997) 417-426
11. Sauer M., Drexhage K.H., Lieberwirth U., Müller R., Nord S., and Zander C. Dynamics of electron-transfer reactions between xanthene dyes and DNA nucleotides monitored on the single molecule level. Chem. Phys. Lett. 284 (1998) 153-163
12. Heinlein T., Knemeyer J.P., Piestert O., and Sauer M. Photoinduced electron transfer between fluorescent dyes and guanosine residues in DNA hairpins. J. Phys. Chem. 107 (2003) 7957-7964
13. Lieberwirth U., Arden-Jacob J., Drexhage K.H., Herten D.P., Müller R., Neumann M., Schultz A., Siebert S., Sanger G., Klingel S., Sauer M., and Wolfrum J. Multiplex dye DNA sequencing in capillary gel electrophoresis (CGE) with diode laser based time-resolved fluorescence detection. Anal. Chem. 70 (1998) 4771-4779
14. Nazarenko I., Lowe B., Darfler M., Ikonomi P., Schuster D., and Rashtchian A. Multiplex quantitative PCR using self-quenched primers labeled with a single fluorophore. Nucleic Acids Res. 30 (2002) e37
15. Kurata S., Kanagawa T., Yamada K., Torimura M., Yokomaku T., Kamagata Y., and Kurane R. Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY FL-labeled probe or primer. Nucleic Acids Res. 29 (2001) e34
16. Shafirovich V.Y., Courtney S.H., Ya N., and Geacintov N.E. Proton coupled photoinduced electron transfer, deuterium isotope effects, and fluorescence quenching in noncovalent benzo-[a]pyrenetetraol-nucleoside complexes in aqueous solutions. J. Am. Chem. Soc. 117 (1995) 4920-4929
17. Lewis F.D., Letsinger R.L., and Wasielewski M.R. Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc. Chem. Res. 34 (2001) 159-170
18. Steenken S., and Jovanovic V. How easily oxidizable is DNA? One-electron reduction potentials of adenosine and guanosine radicals in aqueous solution. J. Am. Chem. Soc. 119 (1997) 617-618
19. Marras S.A.E., Kramer F.R., and Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res. 30 (2002) e122
20. O'Neill M.A., and Barton J.K. Effects of strand and directional asymmetry on base-base coupling and charge transfer in double-helical DNA. Proc. Natl. Acad. Sci. USA 99 (2002) 16543-16550
21. O'Neill M.A., and Barton J.K. 2-Aminopurine: A probe of structural dynamics and charge transfer in DNA and DNA:RNA hybrids. J. Am. Chem. Soc. 124 (2002) 13053-13066
22. Kelley S.O., and Barton J.K. Electron transfer between bases in double helical DNA. Science 283 (1999) 375-381
23. Kimura T., Kawai K., and Majima T. Fluorescence properties of 2- aminopurine-cytidine-7-deazaguanine (5′-ApCdzG-3′) trimer in B- and Z-DNA. Chem. Commun. (Camb.) 3 (2004) 268-269