In vitro selection of molecular beacons

Nucleic Acids Research

Volumn 31, Issue 19, 2003, Pages 5700-5713

  Rajendran, Manjula ^a   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; OLIGONUCLEOTIDE; FLUORESCENT DYE;

ARTICLE; BINDING ASSAY; CONTROLLED STUDY; DNA SEQUENCE; FLUORESCENCE ANALYSIS; GENE AMPLIFICATION; GENE TARGETING; GENETIC ENGINEERING; IN VITRO STUDY; MOLECULAR PROBE; NUCLEIC ACID ANALYSIS; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; AFFINITY CHROMATOGRAPHY; CHEMISTRY; CONFORMATION; ISOLATION AND PURIFICATION; MOLECULAR GENETICS; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; SPECTROFLUOROMETRY;

BASE SEQUENCE; CHROMATOGRAPHY, AFFINITY; FLUORESCENT DYES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; OLIGONUCLEOTIDES; SPECTROMETRY, FLUORESCENCE;

EID: 0142009646     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg764     Document Type: Article

References (45)

1. Tyagi,S. and Kramer,F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
2. Nutiu,R. and Li,Y. (2002) Tripartite molecular beacons. Nucleic Acids Res., 30, E94.
3. Marras,S.A., Kramer,F.R. and Tyagi,S. (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal., 14, 151-156.
4. Marras,S.A., Kramer,F.R. and Tyagi,S. (2003) Genotyping SNPs with molecular beacons. Methods Mol. Biol., 212, 111-128.
5. Kostrikis,L.G., Tyagi,S., Mhlanga,M.M., Ho,D.D. and Kramer,F.R. (1998) Spectral genotyping of human alleles. Science, 279, 1228-1229.
6. Vet,J.A., Majithia,A.R., Marras,S.A., Tyagi,S., Dube,S., Poiesz,B.J. and Kramer,F.R. (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc. Natl Acad. Sci. USA, 96, 6394-6399.
7. Piatek,A.S., Tyagi,S., Pol,A.C., Telenti,A., Miller,L.P., Kramer,F.R. and Alland,D. (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol., 16, 359-363.
8. Tyagi,S., Bratu,D.P. and Kramer,F.R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol., 16, 49-53.
9. Leone,G., van Schijndel,H., van Gemen,B., Kramer,F.R. and Schoen,C.D. (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res., 26, 2150-2155.
10. Sokol,D.L., Zhang,X., Lu,P. and Gewirtz,A.M. (1998) Real time detection of DNA.RNA hybridization in living cells. Proc. Natl Acad. Sci. USA, 95, 11538-11543.
11. Perlette,J. and Tan,W. (2001) Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal. Chem., 73, 5544-5550.
12. Liu,X. and Tan,W. (1999) A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal. Chem., 71, 5054-5059.
13. Liu,X., Farmerie,W., Schuster,S. and Tan,W. (2000) Molecular beacons for DNA biosensors with micrometer to submicrometer dimensions. Anal. Biochem., 283, 56-63.
14. Steemers,F.J., Ferguson,J.A. and Walt,D.R. (2000) Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat. Biotechnol., 18, 91-94.
15. Stojanovic,M.N., de Prada,P. and Landry,D.W. (2001) Catalytic molecular beacons. Chembiochem, 2, 411-415.
16. Stojanovic,M.N., Mitchell,T.E. and Stefanovic,D. (2002) Deoxyribozyme-based logic gates. J. Am. Chem. Soc., 124, 3555-3561.
17. Li,J., Fang,X., Schuster,S., Liu,X. and Tan,W. (2000) Molecular beacons: a novel approach to detect protein-DNA interactions. Angew. Chem. Int. Ed. Engl., 39, 1049-1052.
18. Fang,X., Li,J.J. and Tan,W. (2000) Using molecular beacons to probe molecular interactions between lactate dehydrogenase and single-stranded DNA. Anal. Chem., 72, 3280-3285.
19. Heyduk,T. and Heyduk,E. (2002) Molecular beacons for detecting DNA binding proteins. Nat. Biotechnol., 20, 171-176.
20. Hesselberth,J., Robertson,M.P., Jhaveri,S. and Ellington,A.D. (2000) In vitro selection of nucleic acids for diagnostic applications. Rev. Mol. Biotechnol., 74, 15-25.
21. Jayasena,S.D. (1999) Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem., 45, 1628-1650.
22. Wilson,D.S. and Szostak,J.W. (1999) In vitro selection of functional nucleic acids. Annu. Rev. Biochem., 68, 611-647.
23. Rajendran,M. and Ellington,A.D. (2002) Nucleic acids for reagentless biosensors. In Ligler,F.S. and Rowe Taitt,C.A. (eds), Optical Biosensors: Present and Future. Elsevier Science BV, Amsterdam, pp. 369-396.
24. Rajendran,M. and Ellington,A.D. (2002) Selecting nucleic acids for biosensor applications. Comb. Chem. High Throughput Screen., 5, 263-270.
25. Jhaveri,S., Kirby,R., Conrad,R., Maglott,E.J., Bowser,M., Kennedy,R.T., Glick,G. and Ellington,A.D. (2000) Designed signaling aptamers that transduce molecular recognition to changes in fluorescence intensity. J. Am. Chem. Soc., 122, 2469-2473.
26. Li,J.J., Fang,X. and Tan,W. (2002) Molecular aptamer beacons for real-time protein recognition. Biochem. Biophys. Res. Commun., 292, 31-40.
27. Stojanovic,M.N., de Prada,P. and Landry,D.W. (2001) Aptamer-based folding fluorescent sensor for cocaine. J. Am. Chem. Soc., 123, 4928-4931.
28. Hamaguchi,N., Ellington,A. and Stanton,M. (2001) Aptamer beacons for the direct detection of proteins. Anal. Biochem., 294, 126-131.
29. Yamamoto,R., Baba,T. and Kumar,P.K. (2000) Molecular beacon aptamer fluoresces in the presence of Tat protein of HIV-1. Genes Cells, 5, 389-396.
30. Stojanovic,M.N., de Prada,P. and Landry,D.W. (2000) Fluorescent sensors based on aptamer self-assembly. J. Am. Chem. Soc., 122, 11547-11548.
31. Nutiu,R. and Li,Y. (2003) Structure-switching signaling aptamers. J. Am. Chem. Soc., 125, 4771-4778.
32. Jhaveri,S., Rajendran,M. and Ellington,A.D. (2000) In vitro selection of signaling aptamers. Nat. Biotechnol., 18, 1293-1297.
33. Robertson,M.P. and Ellington,A.D. (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat. Biotechnol., 17, 62-66.
34. Cox,J.C., Hayhurst,A., Hesselberth,J., Bayer,T.S., Georgiou,G. and Ellington,A.D. (2002) Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res., 30, e108.
35. Zhang,P., Beck,T. and Tan,W. (2001) Design of a molecular beacon DNA probe with two fluorophores. Angew. Chem. Int. Ed. Engl., 40, 402-405.
36. Nutiu,R. and Li,Y. (2002) Tripartite molecular beacons. Nucleic Acids Res., 30, e94.
37. Tan,W., Fang,X., Li,J. and Liu,X. (2000) Molecular beacons: a novel DNA probe for nucleic acid and protein studies. Chemistry, 6, 1107-1111.
38. Poddar,S.K. (1999) Detection of adenovirus using PCR and molecular beacon. J. Virol. Methods, 82, 19-26.
39. 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.
40. Li,Q., Luan,G., Guo,Q. and Liang,J. (2002) A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Res., 30, e5.
41. Green,R., Ellington,A.D., Bartel,D.P. and Szostak,J.W. (1991) In vitro genetic analysis: selection and amplification of rare functional nucleic acids. Methods, 2, 75-86.
42. Tyagi,S., Marras,S.A. and Kramer,F.R. (2000) Wavelength-shifting molecular beacons. Nat. Biotechnol., 18, 1191-1196.
43. Seeman,N.C. (2003) DNA in a material world. Nature, 421, 427-431.
44. Yurke,B., Turberfield,A.J., Mills,A.P.,Jr, Simmel,F.C. and Neumann,J.L. (2000) A DNA-fuelled molecular machine made of DNA. Nature, 406, 605-608.
45. Alberti,P. and Mergny,J.L. (2003) DNA duplex-quadruplex exchange as the basis for a nanomolecular machine. Proc. Natl Acad. Sci. USA, 100, 1569-1573.