Novel DNA probes with low background and high hybridization-triggered fluorescence

Nucleic Acids Research

Volumn 35, Issue 5, 2007, Pages

  Lukhtanov, Eugeny A ^a   Lokhov, Sergey G ^a,b   Gorn, Vladimir V ^a   Podyminogin, Mikhail A ^a,c   Mahoney, Walt ^a  

^a Nanogen Inc Bothell   (United States)

^b Cepheid   (United States)

^c INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL REACTION KINETICS; CHEMICAL STRUCTURE; COMPARATIVE STUDY; DNA HYBRIDIZATION; DNA PROBE; FLUORESCENCE ANALYSIS; MOLECULAR BEACON; MOLECULAR INTERACTION; PHOTOCHEMICAL QUENCHING; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SIGNAL NOISE RATIO; TEMPERATURE DEPENDENCE; CHEMISTRY; KINETICS; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE;

FLUORESCENT DYE;

DNA PROBES; FLUORESCENT DYES; KINETICS; NUCLEIC ACID HYBRIDIZATION; TEMPERATURE;

EID: 34247168413     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1136     Document Type: Article

References (42)

1. Tyagi,S. and Kramer,F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
2. Marras,S.A.E., Kramer,F.R. and Tyagi,S. (2002) Efficiency of fluorescence energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res., 30, e122.
3. Whitcombe,D., Theaker,J., Guy,S.P., Brown,T. and Little,S. (1999) Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol., 17, 804-807.
4. Armitage,B., Ly,D., Koch,T., Frydenlund,H., Orum,H. and Schuster,G.B. (1998) Hairpin-forming peptide nucleic acid oligomers. Biochemistry 37, 9417-9425.
5. Coull,J.M., Gildea,B.D. and Hyldig-Nielsen,J.J. (1999). Methods, kits and compositions pertaining to PNA molecular beacons. WO A-9922018.
6. Livak,K.J., Flood,S.J.A., Marmaro,J., Giusti,W. and Deetz,K. (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR products and nucleic acid hybridization. PCR Methods Appl., Cold Spring Harbor Laboratory Press, 4, 357-362.
7. Livak,K.J., Flood,S.J.A., Mamoro,J. and Mullah,K.B. (2004). Hybridization assay using self-quenching fluorescence probe. US6821727 B1.
8. Kuhn,H., Demidov,V.V., Coull,J.M., Fiandaca,M.J., Gildea,B.D. and Frank-Kamenetskii,M.D. (2002) Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets. J. Am. Chem. Soc., 124, 1097-1103.
9. Gildea,B.D., Coull,J.M., Hyldig-Nielsen,J.J. and Fiandaca, M.J. (1999). Methods, kits and compositions pertaining to linear beacons. WO A-9921881.
10. Seitz,O. (2000) Solid-phase synthesis of doubly labeled peptide nucleic acids as probes for the real-time detection of hybridization. Angew. Chem., International Edition, 39, 3249-3252.
11. Johansson,M.K., Fidder,H., Dick,D. and Cook,R.M. (2002) Intramolecular dimers: A new strategy to fluorescence quenching in dual-labeled oligonucleotide probes. J. Am. Chem. Soc., 124, 6950-6956.
12. Davies,M., Bruce,I.M. and Wolter,A. Nucleic acid probes and methods to detect and/or quantify nucleic acid analytes (2003) US patent application 0143591 A1.
13. Ranasinghe,R.T., Brown,L.J. and Brown,T. (2001) Linear fluorescent oligonucleotide probes with an acridine quencher generate a signal upon hybridization. Chem. Commun., 1480-1481.
14. Yamane,A. (2002) MagiProbe: A novel fluorescence quenching-based oligonucleotide probe carrying a fluorophore and an intercalator. Nucleic Acids Res., 30, e97.
15. Kodama,S., Asano,S., Moriguchi,T., Sawai,H. and Shinozuka,K. (2006) Novel fluorescent oligoDNA probe bearing a multiconjugated nucleoside with a fluorophore and a non-fluorescent intercalator as a quencher. Bioorg. Med. Chem. Lett., 16, 2685-2688.
16. Ishiguro,T., Saitoh,J., Yawata,H., Otsuka,M., Inoue,T. and Sugiura,Y. (1996) Fluorescence detection of specific sequence of nucleic acids by oxazole yellow-linked oligonucleotides. Homogeneous quantitative monitoring of in vitro transcription. Nucleic Acids Res., 24 4992-4997.
17. Svanvik,N., Westman,G., Wang,D. and Kubista,M. (2000) Light-up probes: Thiazole orange-conjugated peptide nucleic acid for detection of target nucleic acid in homogeneous solution. Anal. Biochem., 281, 26-35.
18. Kohler,O., Jarikote,D.V. and Seitz,O. (2005) Forced intercalation probes (FIP): Thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection. Chem. Bio. Chem., 6, 69-77.
19. Marks,A.H., Bhadra,P.K., McDowell,D.G., French,D.J., Douglas,K.T., Bichenkova,E.V. and Bryce,R.A. (2005) Molecular basis of action of HyBeacon fluorogenic probes: A spectroscopic and molecular dynamics study. J. Biomol. Struct. Dyn., 23, 49-62.
20. Knemeyer,J.P., Marme,N. and Sauer,M. (2000) Probes for detection of specific DNA sequences at the single-molecule level. Anal. Chem., 72, 3717-3724.
21. Crockett,A.O. and Wittwer,C.T. (2001) Fluorescein-labeled oligonucleotides for real-time pcr: Using the inherent quenching of deoxyguanosine nucleotides. Anal. Biochem., 290, 89-97.
22. Kurata,S., Kanagawa,T., Yamada,K., Torimura,M., Yokomaku,T., Kamagata,Y. and Kurane,R. (2001) Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY((R)) FL-labeled probe or primer. Nucleic Acids Res., 29, E34.
23. Kutyavin,I.V., Afonina,I.A., Mills,A., Gorn,V.V., Lukhtanov,E.A., Belousov,E.S., Singer,M.J., Walburger,D.K., Lokhov,S.G. et al. (2000) 3′-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res., 28, 655-661.
24. Reed,M.W., Lukhtanov,E.A., Gall,A.A and Dempcy,R.O. (2004). Fluorescent quenching detection reagents and methods. US6727356.
25. Holland,P.M., Abramson,R.D., Watson,R. and Gelfand,D.H. (1991). Detection of specific polymerase chain reaction product using the 5′ to 3′ exonuclease activity of thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. U.S.A., 88, 7276-7280.
26. Lyamichev,V., Brown,M.A.D. and Dahlberg,J.E. (1993) Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science, 260, 778-783.
27. Afonina,I.A., Lokhov,S.G., Belousov,Y.S., Reed,M.W., Lukhtanov,E.A., Shishkina,I.G., Gorn,V.V., Sanders,S.M., Walburger,D.K. et al. (2002) Hybridization-triggered fluorescence detection of DNA with minor groove binder-conjugated probes. Proc. SPIE, 4626, 322-331.
28. Afonina,I.A., Reed,M.W., Lusby,E., Shishkina,I.G. and Belousov,Y.S. (2002) Minor groove binder-conjugated DNA probes for quantitative DNA detection by hybridization-triggered fluorescence. BioTechniques, 32, 940-944.
29. Lokhov,S. and Lukhtanov,E. (2005). Fluorescent probes for DNA detection by hybridization with improved sensitivity and low background. US Patent Application, 2005/0214797 A1
30. Reed,M.W., Lukhtanov,E.A., Gall,A.A., Dempcy,R.O. and Vermeulen,N.M.J. (2004). Fluorescent quenching detection reagents and methods. US6790945.
31. Cantor,C.R., Warshaw,M.M. and Shapiro,H. (1970) Oligonucleotide interaction III. Circular dicroism studies of the conformation of deoxyoligonucleotides. Biopolymers, 9, 1059-1077.
32. Bonnet,G., Tyagi,S., Libchaber,A. and Kramer,F.R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. U.S.A., 96, 6171-6176.
33. Tsourkas,A., Behlke,M.A., Rose,S.D. and Bao,G. (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res. 31, 1319-1330.
34. Edman,L., Mets,U. and Rigler,R. (1996) Conformational transitions monitored for single molecules in solution. Proc. Natl. Acad. Sci., U.S.A., 93, 6710-6715.
35. Torimura,M., Kurata,S., Yamada,K., Yokomaku,T., Kamagata,Y., Kanagawa,T. and Kurane,R. (2001) Fluorescence-quenching phenomenon by photoinduced electron transfer between fluoresc dye and a nucleotide base. Anal. Sci., 17, 155-160.
36. Lay,M.J. and Wittwer,C.T. (1997) Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clin. Chem., 43, 2262-2267.
37. Wittwer,C.T., Herrmann,M.G., Gundry,C.N. and Elenitoba-Johnson,K.S.J. (2001) Real-time multiplex PCR assays. Methods, 25, 430-442.
38. Afonina,I.A., Belousov,Y.S., Metcalf,M., Mills,A., Sanders,S., Walburger,D.K., Mahoney,W. and Vermeulen,N.M.J. (2004) Single nucleotide polymorphism detection with fluorescent MGB MGB-Eclipse probe systems. In: Bustin,S.A. (ed), A-Z of Quantitative PCR. 11, 265-270.
39. Fang,X., Liu,X., Schuster,S. and Tan,W. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J. Am. Chem. Soc., 121, 2921-2922.
40. Wang,H., Li,J., Liu,H., Liu,Q., Mei,Q., Wang,Y., Zhu,J., He,N. and Lu,Z. (2002) Label-free hybridization detection of a single nucleotide mismatch by immobilization of molecular beacons on an agarose film. Nucleic Acids Res., 30, e61.
41. Ramachandran,A., Flinchbaugh,J., Ayoubi,P., Olah,G.A. and Malayer,J. (2004) Target discrimination by surface-immobilized beacons designed to detect. Francisella tularensis. Biosens. Bioelectron., 19, 727-736.
42. Kutyavin,I., Lokhov,S., Lukhtanov,E. and Reed,M.W. (2003) Chemistry of minor groove binder - oligonucleotide conjugates. Current Protocols in Nucleic Acid Chemistry, John Wiley & Sons, Inc., Hoboken, NJ, 8.4.1-8.4.21.