New approach to real-time nucleic acids detection: Folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of Förster resonance energy transfer probes in 5′-nuclease assays

Nucleic Acids Research

Volumn 38, Issue 5, 2009, Pages

  Kutyavin, Igor V ^a  

^a Perpetual Genomics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; NUCLEIC ACID; FLUORESCENT DYE; PRIMER DNA; TAQ POLYMERASE;

AMPLICON; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SUBSTRATE; FLUORESCENCE ANALYSIS; FLUORESCENCE RESONANCE ENERGY TRANSFER; HYBRIDIZATION; INTERMETHOD COMPARISON; MOLECULAR BEACON; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN CLEAVAGE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; REAL TIME POLYMERASE CHAIN REACTION; SIGNAL DETECTION; SINGLE NUCLEOTIDE POLYMORPHISM; THERMUS AQUATICUS; CHEMISTRY; CONFORMATION; EVALUATION; METHODOLOGY; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION;

SCORPIONES; THERMUS AQUATICUS;

DNA PRIMERS; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; OLIGONUCLEOTIDE PROBES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; TAQ POLYMERASE;

EID: 77951655043     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1138     Document Type: Article

References (37)

1. Higuchi,R., Dollinger,G., Walsh,P.S. and Griffith,R. (1992) Simultaneous amplification and detection of specific DNA sequences. Biotechnology, 10, 413-417.
2. Higuchi,R., Fockler,C., Dollinger,G. and Watson,R. (1993) Kinetic PCR: Real time monitoring of DNA amplification reactions. Biotechnology, 11, 1026-1030.
3. Morrison,T.B., Weis,J.J. and Wittwer,C.T. (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. Biotechnologies, 24, 954-958.
4. Förster,T. (1965) Delocalized excitation and excitation transfer. In Sinanoglu,O. (ed.), Modern Quantum Chemistry, Istanbul Lectures, part III. Academic Press, New York, pp. 93-137.
5. Clegg,R.M. (1992) Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol., 211, 353-388.
6. Didenko,V.V. (2001) DNA probes using fluorescence resonance energy transfer (FRET): design and application. Bio Techniques, 31, 1106-1121.
7. Livak,K.J., Flood,S.J.A., Marmaro,J. and Mullah,K.B. (1998) Self-quenching fluorescent probe. US Patent, 5, 723, 591.
8. 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. Bio Techniques, 32, 940-949.
9. Ortiz,E., Estrada,G. and Lizardi,P.M. (1998) PNA molecular beacons for rapid detection of PCR amplicons. Mol. Cell. Probes, 12, 219-226.
10. Tyagi,S. and Kramer,F.R. (1996) Molecular beacons-probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
11. 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.
12. Duck,P., Bender,R., Crosby,W. and Robertson,J.G. (1989) Nucleic acid compositions with scissile linkage useful for detecting nucleic acid sequences. US Patent., 4, 876, 187.
13. Harvey,J.J., Lee,S.P., Chan,K., Kim,J.H., Hwang,E.-S., Cha,C.-Y., Knutson,J.R. and Han,M.K. (2004) Characterization and application of CataCleave probe in real-time detection assays. Anal. Biochem., 333, 246-255.
14. Kutyavin,I.V., Milesi,D., Belousov,Y., Podyminogin,M., Vorobiev,A., Gorn,V., Lukhtanov,E.A., Vermeulen,N.M.J. and Mahoney,W. (2006) A novel endonuclease IV post-PCR genotyping system. Nucleic Acids Res., 34, e128.
15. Gelfand,D.H., Holland,P.M., Saiki,R.K. and Watson,R.M. (1993) Homogeneous assay system using the nuclease activity of a nucleic acid polymerase. US Patent., 5, 210, 015.
16. Lie,Y.S. and Petropoulos,C.J. (1998) Advances in quantitative PCR technology: 5′ nuclease assays. Curr. Opin. Biotech., 9, 43-48.
17. Kutyavin,I.V., Lukhtanov,E.A., Gamper,H.B. and Meyer,R.B. (1997) Oligonucleotides with conjugated dihydropyrroloindole tripeptides: base composition and backbone effects on hybridization. Nucleic Acids Res., 25, 3718-3723.
18. 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., Gall,A.A. et al. (2000) 30-Minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res., 28, 655-661.
19. Breslauer,K.J., Frank,R., Blocker,H. and Marky,L.A. (1986) Predicting DNA duplex stability from the base sequence. Proc. Natl Acad. Sci. USA, 83, 3746-3750.
20. SantaLucia,J. Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA, 95, 1460-1465.
21. Allawi,H.T., Kaiser,M.W., Onufriev,A.V., Ma,W.P., Brogaard,A.E., Case,D.A., Neri,B.P. and Lyamichev,V.I. (2003) Modeling of flap endonuclease interactions with DNA substrate. J. Mol. Biol., 328, 537-554.
22. Kaiser,M.W., Lyamicheva,N., Ma,W., Miller,C., Neri,B., Fors,L. and Lyamichev,V.I. (1999) A comparison of Eubacterial and Archaeal structure-specific 5'-exonucleases. J. Biol. Chem., 274, 21387-21394.
23. Gyllensten,U.B. and Erlich,H.A. (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl Acad. Sci. USA, 85, 7652-7656.
24. Cardullo,R.A., Agrawal,S., Flores,C., Zamecnik,P.C. and Wolf,D.E. (1988) Detection of nucleic acid hybridization by nonradioactive fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA, 85, 8790-8804.
25. Lyamichev,V., Mast,A., Hall,J., Prudent,J., Kaiser,M., Takova,T., Kwiatkowski,R., Sander,T., de Arruda,M., Arco,D. et al. (1999) Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol., 17, 292-296.
26. 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. USA, 96, 6171-6176.
27. LaDuca,R.J., Fay,P.J., Chuang,C., McHenry,C.S. and Bambara,R.A. (1983) Site-specific pausing of deoxyribonucleic acid synthesis catalyzed by four forms of Escherichia coli DNA polymerase III. Biochemistry, 22, 5177-5188.
28. Bedinger,P., Munn,M. and Alberts,B.M. (1989) Sequence-specific pausing during in vitro DNA replication on double- stranded DNA templates. J. Biol. Chem., 264, 16880-16886.
29. Bierne,H. and Michel,B. (1994) When replication forks stop. Mol. Microbiol., 13, 17-23.
30. Uhlenbeck,O.C. (1972) Complementary oligonucleotide binding to transfer RNA. J. Mol. Biol., 65, 25-41.
31. Lima,W.F., Monia,B.P., Ecker,D.J. and Freier,S.M. (1992) Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry, 31, 12055-12061.
32. Kutyavin,I. (2007) Use of products of PCR amplification carrying elements of secondary structure to improve PCR-based nucleic acid detection. PCT patent publication, WO/2007/127999.
33. Kutyavin,I.V. (2008) Use of base-modified duplex-stabilizing deoxynucleoside 5'-triphosphates to enhance the hybridization properties of primers and probes in detection polymerase chain reaction. Biochemistry, 47, 13666-13673.
34. Lebedev,Y., Akopyans,N., Azhikina,T., Shevchenko,Y., Potapov,V., Stecenko,D., Berg,D. and Sverdlov,E. (1996) Oligonucleotides containing 2-aminoadenine and 5-methylcytosine are more effective as primers for PCR amplification than their nonmodified counterparts. Genet. Anal., 13, 15-21.
35. Ichihara,Y. and Kurosawa,Y. (1993) Construction of new T vectors for direct cloning of PCR products. Gene, 130, 153-154.
36. Walder,J.A. and Walder,R.Y. (1995) Nucleic acid hybridization and amplification method for detection of specific sequences in which a complementary labeled nucleic acid probe is cleaved. US patent., 5, 403, 711.
37. Duck,P. and McNevin,J. (1997) Cycling probe cleavage detection of nucleic acid sequences. US patent., 5, 660, 988.