Zeptomole detection of a viral nucleic acid using a target-activated ribozyme

RNA

Volumn 9, Issue 9, 2003, Pages 1058-1072

  Vaish, Narendra K ^a   Jadhav, Vasant R ^a   Kossen, Karl ^a   Pasko, Christopher ^a   Andrews, Lori E ^a   McSwiggen, James A ^a   Polisky, Barry ^a   Seiwert, Scott D ^a,b  

^a Sirna Therapeutics Inc   (United States)

^b InterMune Inc   (United States)

Author keywords

Diagnostic; Hepatitis C virus; Nucleic acid; Riboswitch; Ribozyme

Indexed keywords

LIGASE; NUCLEIC ACID; OLIGONUCLEOTIDE; RIBOZYME; SINGLE STRANDED DNA; VIRUS RNA;

ARTICLE; ENZYME ACTIVITY; HEPATITIS C VIRUS; KINETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SEQUENCE; VIRUS GENOME;

HEPACIVIRUS; HYDROGEN-ION CONCENTRATION; RNA, CATALYTIC; RNA, VIRAL; TIME FACTORS;

DNA VIRUSES; HEPATITIS C VIRUS;

EID: 0041331493     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5760703     Document Type: Article

References (49)

1. Araki, M., Okuno, Y., Hara, Y, and Sugiura, Y. 1998. Allosteric regulation of a ribozyme activity through ligand-induced conformational change. Nucleic Acids Res. 26: 3379-3384.
2. Bartel, D.P. and Szostak, J.W. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411-1418.
3. Bergman, N.H., Johnston, W.K., and Bartel, D.P. 2000. Kinetic framework for ligation by an efficient RNA ligase ribozyme. Biochemistry 39: 3115-3123.
4. Breaker, R.R. 2002. Engineered allosteric ribozymes as biosensor components. Curr. Opin. Biotechnol. 13: 31-39.
5. Burke, D.H., Ozerova, N.D., and Nilsen-Hamilton, M. 2002. Allosteric hammerhead ribozyme TRAPs. Biochemistry 41: 6588-6594.
6. Carter, P. and Wells, J.A. 1987. Engineering enzyme specificity by "substrate-assisted catalysis." Science 237: 394-399.
7. Conry-Cantilena, C. 1997. Hepatitis C virus diagnostics: Technology, clinical applications and impacts. Trends Biotechnol. 15: 71-76.
8. Dufour, D.R. 2002. Hepatitis C: Laboratory tests for diagnosis and monitoring of infection. Clinical Lab. News 10,12,14.
9. Ekland, E.H. and Bartel, D.P. 1995. The secondary structure and sequence optimization of an RNA ligase ribozyme. Nucleic Acids Res. 23:3231-3238.
10. -. 1996. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382: 373-376.
11. Ekland, E.H., Szostak, J.W., and Bartel, D.P. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269: 364-370.
12. Fedor, M.J. and Westhof, E. 2002. Ribozymes: The first 20 years. Mol. Cell 10: 703-704.
13. Glasner, M.E., Yen, C.C., Ekland, E.H., and Bartel, D.P. 2000. Recognition of nucleoside triphosphates during RNA-catalyzed primer extension. Biochemistry 39: 15556-15562.
14. Glasner, M.E., Bergman, N.H., and Bartel, D.P. 2002. Metal ion requirements for structure and catalysis of an RNA ligase ribozyme. Biochemistry 41: 8103-8112.
15. Hartig, J.S., Najafi-Shoushtari, S.H., Grune, I., Yan, A., Ellington, A.D., and Famulok, M. 2002. Protein -dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20: 717-722.
16. Hesselberth, J.R., Robertson, M.P., Knudsen, S.M., and Ellington, A.D. 2003. Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal. Biochem. 312: 106-112.
17. Hoffman, D., Hesselberth, J., and Ellington, A.D. 2001. Switching nucleic acids for antibodies. Nat. Biotechnol. 19: 313-314.
18. Iyo, M., Kawasaki, H., and Taira, K. 2002. Allosterically controllable maxizymes for molecular gene therapy. Curr. Opin. Mol. Ther. 4: 154-165.
19. Johnston, W.K., Unrau, P.J., Lawrence, M.S., Glasner, M.E., and Bartel, D.P. 2001. RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension. Science 292: 1319-1325.
20. Koizumi, M., Kerr, J.N., Soukup, G.A., and Breaker, R.R. 1999. Allosteric ribozymes sensitive to the second messengers cAMP and cGMP. Nucleic Acids Symp. Ser. 42: 275-276.
21. Komatsu, Y., Yamashita, S., Kazama, N., and Ohtsuka, E. 1999. Induction of ribozyme activity by anti-ribozyme oligonucleotides. Nucleic Acids Symp. Ser. 42: 279-280.
22. Komatsu, Y., Nobuoka, K., Karino-Abe, N., Matsuda, A., and Ohtsuka, E. 2002. In vitro selection of hairpin ribozymes activated with short oligonucleotides. Biochemistry 41: 9090-9098.
23. Kumar, R.K. and Davis, D.R. 1997. Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res. 25: 1272-1280.
24. Kuwabara, T., Warashina, M., and Taira, K. 2000. Allosterically controllable maxizymes cleave mRNA with high efficiency and specificity. Trends Biotechnol. 18: 462-468.
25. Lebedev, Y., Akopyants, 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.
26. Lorsch, J.R. and Szostak, J.W. 1995. Kinetic and thermodynamic characterization of the reaction catalyzed by a polynucleotide kinase ribozyme. Biochemistry 34: 15315-15327.
27. Majid, A.M. and Gretch, D.R. 2002. Current and future hepatitis C virus diagnostic testing: Problems and advancements. Microbes Infect. 4: 1227-1236.
28. McGinness, K.E., Wright, M.C., and Joyce, G.F. 2002. Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions. Chem. Biol. 9: 585-596.
29. Mei, S.H., Liu, Z., Brennan, J.D., and Li, Y. 2003. An efficient RNA-cleaving DNA enzyme that synchronizes catalysis with fluorescence signaling. J. Am. Chem. Soc. 125:412-420.
30. Porta, H. and Lizardi, P.M. 1995. An allosteric hammerhead ribozyme. Biotechnology (N Y) 13: 161-164.
31. Rajendran, M. and Ellington, A.D. 2002. Selecting nucleic acids for biosensor applications. Comb. Chem. High Throughput Screen. 5: 263-270.
32. Reich, C., Olsen, G.J., Pace, B., and Pace, N.R. 1988. Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science 239: 178-181.
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. -. 2000. Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res. 28: 1751-1759.
35. -. 2001. In vitro selection of nucleoprotein enzymes. Nat. Biotechnol. 19: 650-655.
36. Rohatgi, R., Bartel, D.P., and Szostak, J.W. 1996. Kinetic and mechanistic analysis of nonenzymatic, template-directed oligoribonucleotide ligation. J. Am. Chem. Soc. 118: 3332-3339.
37. Schneider, T.D. and Stephens, R.M. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100.
38. Seetharaman, S., Zivarts, M., Sudarsan, N., and Breaker, R.R. 2001. Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol. 19: 336-341.
39. Soukup, G.A. and Breaker, R.R. 1999. Design of allosteric hammer-head ribozymes activated by ligand-induced structure stabilization. Structure Fold. Des. 7: 783-791.
40. Stojanovic, M.N., de Prada, P., and Landry, D.W. 2001. Catalytic molecular beacons. Chembiochem 2: 411-415.
41. Tang, J. and Breaker, R.R. 1997. Rational design of allosteric ribozymes. Chem. Biol. 4: 453-459.
42. Vaish, N.K., Dong, F., Andrews, L., Schweppe, R.E., Ahn, N.G., Blatt, L., and Seiwert, S.D. 2002. Monitoring post- translational modification of proteins with allosteric ribozymes. Nat. Biotechnol. 20: 810-815.
43. Verma, S. and Eckstein, F. 1998. Modified oligonucleotides: Synthesis and strategy for users. Annu. Rev. Biochem, 67: 99-134.
44. Wang, D.Y. and Sen, D. 2001. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. J. Mol. Biol. 310: 723-734.
45. -. 2002. Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Comb. Chem. High Throughput Screen. 5: 301-312.
46. Wang, D.Y., Lai, B.H., and Sen, D. 2002a. A general strategy for effector-mediated control of RNA-cleaving ribozymes and DNA enzymes. J. Mol. Biol. 318: 33-43.
47. Wang, D.Y., Lai, B.H., Feldman, A.R., and Sen, D. 2002b. A general approach for the use of oligonucleotide effectors to regulate the catalysis of RNA-cleaving ribozymes and DNAzymes. Nucleic Acids Res. 30: 1735-1742.
48. Wright, M.C. and Joyce, G.F. 1997. Continuous in vitro evolution of catalytic function. Science 276: 614-617.
49. Xia, T., SantaLucia Jr. J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Jiao, X., Cox, C., and Turner, D.H. 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37:14719-14735.