Monitoring helicase activity with molecular beacons

BioTechniques

Volumn 45, Issue 4, 2008, Pages 433-442

  Belon, Craig A ^a   Frick, David N ^a  

^a NEW YORK MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYANINE DYE 3; CYANINE DYE 5; HELICASE; OLIGONUCLEOTIDE; CARBOCYANINE; DNA; NS3 PROTEIN, HEPATITIS C VIRUS; RNA; VIRUS PROTEIN;

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA EXTRACTION; DNA STRAND; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME SPECIFICITY; FLUORESCENCE; GENE SEQUENCE; HEPATITIS C VIRUS; HIGH THROUGHPUT SCREENING; MOLECULAR BEACON; MOLECULAR BEACON HELICASE ASSAY; CONFORMATION; ENZYMOLOGY; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC PROCEDURES; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; VIRUS GENOME;

HEPATITIS C VIRUS;

BASE SEQUENCE; CARBOCYANINES; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENOME, VIRAL; HEPACIVIRUS; MOLECULAR PROBE TECHNIQUES; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; VIRAL NONSTRUCTURAL PROTEINS;

EID: 55949107966     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000112834     Document Type: Article

References (34)

1. Singleton, M.R., M.S. Dillingham, and D.B. Wigley. 2007. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76:23-50.
2. Frick, D.N. and A.M. Lam. 2006. Understanding helicases as a means of virus control. Curr. Pharm. Des. 12:1315-1338.
3. Matson, S.W., S. Tabor, and C.C. Richardson. 1983. The gene 4 protein of bacteriophage T7. Characterization of helicase activity. J. Biol. Chem. 258:14017-14024.
4. Sivaraja, M., H. Giordano, and M.G. Peterson. 1998. High-throughput screening assay for helicase enzymes. Anal. Biochem. 265:22-27.
5. Earnshaw, D.L. and A.J. Pope. 2001. FlashPlate scintillation proximity assays for characterization and screening of DNA polymerase, primase, and helicase activities. J. Biomol. Screen. 6:39-46.
6. Zhang, L., G. Schwartz, M. O'Donnell, and R.K. Harrison. 2001. Development of a novel helicase assay using electrochemiluminescence. Anal. Biochem. 293:31-37.
7. Raney, K.D., L.C. Sowers, D.P. Millar, and S.J. Benkovic. 1994. A fluorescence-based assay for monitoring helicase activity. Proc. Natt. Acad. Sci. USA 91:6644-6648.
8. Houston, P. and T. Kodadek. 1994. Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA. Proc. Natl. Acad. Sci. USA 91:5471-5474.
9. Bjornson, K.P., M. Amaratunga, K.J. Moore, and T.M. Lohman. 1994. Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer. Biochemistry 33:14306-14316.
10. Earnshaw, D.L., K.J. Moore, C.J. Greenwood, H. Djaballah, A.J. Jurewicz, K.J. Murray, and A.J. Pope. 1999. Time-resolved fluorescence energy transfer DNA helicase assays for high throughput screening. J. Biomol. Screen. 4:239-248.
11. Eggleston, A.K., N.A. Rahim, and S.C. Kowalczykowski. 1996. A helicase assay based on the displacement of fluorescent, nucleic acid-binding ligands. Nucleic Acids Res. 24:1179-1186.
12. Tyagi, S. and F.R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
13. Delagoutte, E. and P.H. Yon Hippel. 2002. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part I: Structures and properties of isolated helicases. Q. Rev. Biophys. 35:431-478.
14. Patel, S.S. and I. Donmez. 2006. Mechanisms of helicases. J. Biol. Chem. 281:18265-18268.
15. Frick, D.N. 2007. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr. Issues Mol. Biol. 9:1-20.
16. Kolykhalov, A.A., K. Mihalik, S.M. Feinstone, and C.M. Rice. 2000. Hepatitis C virus-encoded enzymatic activities and conserved RNA elements in the 3′ nontranslated region are essential for virus replication in vivo. J. Virol. 74:2046-2051.
17. Lam, A.M. and D.N. Frick. 2006. Hepatitis C virus subgenomic replicon requires an active NS3 RNA helicase. J. Virol. 80:404-411.
18. Borowski, P., J. Deinert, S. Schalinski, M. Bretner, K. Ginalski, T. Kulikowski, and D. Shugar. 2003. Halogenated benzimidazoles and benzotriazoles as inhibitors of the NTPase/helicase activities of hepatitis C and related viruses. Eur. J. Biochem. 270:1645-1653.
19. Maga, G., S. Gemma, C. Fattorusso, G.A. Locatelli, S. Butini, M. Persico, G. Kukreja, M.P. Romano, et al. 2005. Specific targeting of hepatitis C virus NS3 RNA helicase. Discovery of the potent and selective competitive nucleotide-mimicking inhibitor QU663. Biochemistry 44:9637-9644.
20. Boguszewska-Chachulska, A.M., M. Krawczyk, A. Najda, K. Kopanska, A. Stankiewicz-Drogon, W. Zagorski-Ostoja, and M. Bretner. 2006. Searching for a new anti-HCV therapy: Synthesis and properties of tropolone derivatives. Biochem. Biophys. Res. Commun. 341:641-647.
21. Borowski, P., M. Lang, A. Haag, and A. Baier. 2007. Tropolone and its derivatives as inhibitors of the helicase activity of hepatitis C virus nucleotide triphosphatase/helicase. Antivir. Chem. Chemother. 18:103-109.
22. Hsu, C.C., L.H. Hwang, Y.W. Huang, W.K. Chi, Y.D. Chu, and D.S. Chen. 1998. An ELISA for RNA helicase activity: application as an assay of the NS3 helicase of hepatitis C virus. Biochem. Biophys. Res. Commun. 253:594-599.
23. Kyono, K., M. Miyashiro, and I. Taguchi. 1998. Detection of hepatitis C virus helicase activity using the scintillation proximity assay system. Anal. Biochem. 257:120-126.
24. Hicham Alaoui-Ismaili, M., C. Gervais, S. Brunette, G. Gouin, M. Hamel, R.F. Rando, and J. Bedard. 2000. A novel high throughput screening assay for HCV NS3 helicase activity. Antiviral Res. 46:181-193.
25. Porter, D.J., S.A. Short, M.H. Hanlon, F. Preugschat, J.E. Wilson, D.H.J. Willard, and T.G. Consler. 1998. Product release is the major contributor to kcat for the hepatitis C virus helicase-catalyzed strand separation of short duplex DNA. J. Biol. Chem. 273:18906-18914.
26. Boguszewska-Chachulska, A.M., M. Krawczyk, A. Stankiewicz, A. Gozdek, A.L. Haenni, and L. Strokovskaya. 2004. Direct fluorometric measurement of hepatitis C virus helicase activity. FEBS Lett. 567:253-258.
27. Lam, A.M., D. Keeney, P.Q. Eckert, and D.N. Frick. 2003. Hepatitis C virus NS3 ATPases/helicases from different genotypes exhibit variations in enzymatic properties. J. Virol. 77:3950-3961.
28. Zhang, J.H., T.D. Chung, and K.R. Oldenburg. 1999. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen. 4:67-73.
29. Santangelo, P.J., B. Nix, A. Tsourkas, and G. Bao. 2004. Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res. 32:e57.
30. Gwack, Y., D.W. Kim, J.H. Han, and J. Choe. 1997. DNA helicase activity of the hepatitis C virus nonstructural protein 3. Eur. J. Biochem. 250:47-54.
31. Levin, M.K., Y.H. Wang, and S.S. Patel. 2004. The functional interaction of the hepatitis C virus helicase molecules is responsible for unwinding processivity. J. Biol. Chem. 279:26005-26012.
32. Wong, I., K.L. Chao, W. Bujalowski, and T.M. Lohman. 1992. DNA-induced dimerization of the Escherichia coli rep helicase. Allosteric effects of single-stranded and duplex DNA. J. Biol. Chem. 267:7596-7610.
33. Gozdek, A., I. Zhukov, A. Polkowska, J. Poznanski, A. Stankiewicz-Drogon, J.M. Pawlowicz, W. Zagorski-Ostoja, P. Borowski, and A.M. Boguszewska-Chachulska. 2008. NS3 peptide, a novel potent Hepatitis C virus NS3 helicase inhibitor, its mechanism of action and antiviral activity in the replicon system. Antimicrob. Agents Chemother. 52:393-401.
34. Beran, R.K., M.M. Bruno, H.A. Bowers, E. Jankowsky, and A.M. Pyle. 2006. Robust translocation along a molecular monorail: the NS3 helicase from hepatitis C virus traverses unusually large disruptions in its track. J. Mol. Biol. 358:974-982.