The dynamic nature of the four-way junction of the hepatitis C virus IRES

RNA

Volumn 9, Issue 7, 2003, Pages 809-820

  Melcher, Sonya E ^a   Wilson, Timothy J ^a   Lilley, David M J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Fluorescence; FRET; RNA folding; RNA structure; Translation

Indexed keywords

DIVALENT CATION; INITIATION FACTOR; MAGNESIUM ION; METAL ION; NUCLEOTIDE; VIRUS RNA;

5' UNTRANSLATED REGION; ARTICLE; CELL JUNCTION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; FLUORESCENCE; FLUORESCENCE RESONANCE ENERGY TRANSFER; GEL ELECTROPHORESIS; HEPATITIS C VIRUS; INTERNAL RIBOSOME ENTRY SITE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INDUCTION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; RIBOSOME SUBUNIT; RNA STRUCTURE; STEADY STATE; STRUCTURE ANALYSIS; TRANSLATION INITIATION;

BASE SEQUENCE; HEPACIVIRUS; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, VIRAL; SPECTROMETRY, FLUORESCENCE;

HEPATITIS C VIRUS;

EID: 0038382863     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.5130703     Document Type: Article

References (35)

1. Alter, H.J., Purcell, R.H., Shih, J.W., Melpolder, J.C., Houghton, M., Choo, Q.L., and Kuo, G. 1989. Detection of antibody to hepatitis C virus in prospectively followed transfusion recipients with acute and chronic non-A, non-B hepatitis. New Engl. J. Med. 321: 1494-1500.
2. Beaucage, S.L. and Caruthers, M.H. 1981. Deoxynucleoside phosphoramidites - a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett. 22: 1859-1862.
3. Brown, E.A., Zhang, H., Ping, L.H., and Lemon, S.M. 1992. Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res. 20: 5041-5045.
4. Choo, Q.L., Kuo, G., Weiner, A.J., Overby, L.R., Bradley, D.W., and Houghton, M. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244: 359-362.
5. Clegg, R.M. 1992. Fluorescence resonance energy transfer and nucleic acids. Meth. Enzymol. 211: 353-388.
6. Clegg, R.M., Murchie, A.I.H., Zechel, A., and Lilley, D.M.J. 1994. The solution structure of the four-way DNA junction at low salt concentration; a fluorescence resonance energy transfer analysis. Biophys. J. 66: 99-109.
7. Cooper, J.P. and Hagerman, P.J. 1987. Gel electrophoretic analysis of the geometry of a DNA four-way junction. J. Mol. Biol. 198: 711-719.
8. De Mitri, M.S., Poussin, K., Baccarini, P., Pontisso, P., D'Errico, A., Simon, N., Grigioni, W., Alberti, A., Beaugrand, M., Pisi, E., et al. 1995. HCV-associated liver cancer without cirrhosis. Lancet 345: 413-415.
9. Duckett, D.R., Murchie, A.I.H., Diekmann, S., von Kitzing, E., Kemper, B., and Lilley, D.M.J. 1988. The structure of the Holliday junction and its resolution. Cell 55: 79-89.
10. Duckett, D.R., Murchie, A.I.H., and Lilley, D.M.J. 1990. The role of metal ions in the conformation of the four-way junction. EMBO J. 9: 583-590.
11. -. (1995). The global folding of four-way helical junctions in RNA, including that in U1 snRNA. Cell 83: 1027-1036.
12. Efron, B. and Tibshirani, R.J. 1993. An introduction to the Bootstrap. Chapman Hall, New York.
13. Eis, P.S. and Millar, D.P. 1993. Conformational distributions of a 4-way DNA junction revealed by time-resolved fluorescence resonance energy transfer. Biochemistry 32: 13852-13860.
14. Fogg, J.M., Kvaratskhelia, M., White, M.F., and Lilley, D.M.J. 2001. Distortion of DNA junctions imposed by the binding of resolving enzymes: A fluorescence study. J. Mol. Biol. 313: 751-764.
15. Förster, T. 1948. Zwischenmolekulare Energiewanderung und Fluoreszenz. Ann. Phys. 2: 55-75.
16. Gough, G.W. and Lilley, D.M.J. 1985. DNA bending induced by cruciform formation. Nature 313: 154-156.
17. Honda, M., Ping, L.H., Rijnbrand, R.C., Amphlett, E., Clarke, B., Rowlands, D.J., and Lemon, S.M. 1996. Structural requirements for initiation of translation by internal ribosome entry within genome-length hepatitis C virus RNA. Virology 222: 31-42.
18. Johnson, M.L. and Faunt, L.M. 1992. Parameter estimation by leastsquares methods. Meth. Enzymol. 210: 1-37.
19. Kieft, J.S., Zhou, K., Grech, A., Jubin, R., and Doudna, J.A. 2002. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struc. Biol. 9: 370-374.
20. Kolupaeva, V.G., Pestova, T.V., and Hellen, C.U. 2000. An enzymatic footprinting analysis of the interaction of 40S ribosomal subunits with the internal ribosomal entry site of hepatitis C virus. J. Virol. 74: 6242-6250.
21. Lakowicz, J.R. 1999. Principles of fluorescence spectroscopy, 2nd ed. Plenum Press, New York.
22. Liang, T.J., Jeffers, L.J., Reddy, K.R., De Medina, M., Parker, I.T., Cheinquer, H., Idrovo, V., Rabassa, A., and Schiff, E.R. 1993. Viral pathogenesis of hepatocellular carcinoma in the United States. Hepatology 18: 1326-1333.
23. Lilley, D.M.J. 2000. Analysis of the global conformation of branched RNA species by a combined electrophoresis and fluorescence approach. Meth. Enzymol. 317: 368-393.
24. Lilley, D.M.J., Clegg, R.M., Diekmann, S., Seeman, N.C., von Kitzing, E., and Hagerman, P. 1995. Nomenclature Committee of the International Union of Biochemistry: A nomenclature of junctions and branchpoints in nucleic acids. Recommendations 1994. Eur. J. Biochem. 230: 1-2.
25. Miick, S.M., Fee, R.S., Millar, D.P., and Chazin, W.J. 1997. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc. Natl. Acad. Sci. 94: 9080-9084.
26. Norman, D.G., Grainger, R.J., Uhrin, D., and Lilley, D.M.J. 2000. The location of Cyanine-3 on double-stranded DNA; importance for fluorescence resonance energy transfer studies. Biochemistry 39: 6317-6324.
27. Nowakowski, J., Shim, P.J., Prasad, G.S., Stout, C.D., and Joyce, G.F. 1999. Crystal structure of an 82 nucleotide RNA-DNA complex formed by the 10-23 DNA enzyme, Nat. Struc. Biol. 6: 151-156.
28. Nowakowski, J., Shim, P.J., Stout, C.D., and Joyce, G.F. 2000. Alternative conformations of a nucleic acid four-way junction, J. Mol. Biol. 300: 93-102.
29. Simonetti, R.G., Camma, C., Fiorello, F., Cottone, M., Rapicetta, M., Marino, L., Fiorentino, G., Craxi, A., Ciccaglione, A., Giuseppetti, R., et al. 1992. Hepatitis C virus infection as a risk factor for hepatocellular carcinoma in patients with cirrhosis. A case-control study. Ann. Intern. Med. 116: 97-102.
30. Sizova, D.V., Kolupaeva, V.G., Pestova, T.V., Shatsky, I.N., and Hellen, C.U. 1998. Specific interaction of eukaryotic translation initiation factor 3 with the 5′ nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. J. Virol. 72: 4775-4782.
31. Spahn, C.M., Kieft, J.S., Grassucci, R.A., Penczek, P.A., Zhou, K., Doudna, J.A., and Frank, J. 2001. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291: 1959-1962.
32. Walter, F., Murchie, A.I.H., Duckett, D.R., and Lilley, D.M.J. 1998a. Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer. RNA 4: 719-728.
33. Walter, F., Murchie, A.I.H., and Lilley, D.M.J. 1998b. The folding of the four-way RNA junction of the hairpin ribozyme. Biochemistry 37: 17629-17636.
34. Wilson, T.J., Zhao, Z.-Y., Maxwell, K., Kontogiannis, L., and Lilley, D.M.J. 2001. Importance of specific nucleotides in the folding of the natural form of the hairpin ribozyme. Biochemistry 40: 2291-2302
35. Yang, M.S. and Millar, D.P. 1996. Conformational flexibility of threeway DNA junctions containing unpaired nucleotides. Biochemistry 35: 7959-7967.