Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates

RNA

Volumn 3, Issue 4, 1997, Pages 392-404

  Walter, Nils G ^a   Burke, John M ^a  

^a UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

Author keywords

anisotropy; dissociation; fluorescence; hybridization; loop loop interaction; pre steady state kinetics; RNA cleavage; single turnover kinetics

Indexed keywords

DNA; FLUORESCEIN; OLIGONUCLEOTIDE; RIBOZYME; RNA;

ANISOTROPY; ARTICLE; CATALYSIS; CONTROLLED STUDY; DISSOCIATION; ENZYME KINETICS; ENZYME SUBSTRATE COMPLEX; PRIORITY JOURNAL; REACTION TIME; RNA CLEAVAGE; SPECTROFLUOROMETRY;

FLUORESCEIN; FLUORESCEINS; GUANOSINE; KINETICS; OLIGORIBONUCLEOTIDES; RNA, CATALYTIC; SPECTROMETRY, FLUORESCENCE;

EID: 0030969442     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (60)

1. Asp catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry 33:10294-10304.
2. Bevilacqua PC, Johnson KA, Turner DH. 1993. Cooperative and anticooperative binding to a ribozyme. Proc Natl Acad Sci USA 90:8357-8361.
3. Bevilacqua PC, Kierzek R, Johnson KA, Turner DH. 1992. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science 258:1355-1358.
4. Bevilacqua PC, Li Y, Turner DH. 1994. Fluorescence-detected stopped flow with a pyrene-labeled substrate reveals that guanosine facilitates docking of the 5′ cleavage site into a high free energy binding mode in the Tetrahymena ribozyme. Biochemistry 33:11340-11348.
5. Bjornson KP, Amaratunga M, Moore KJH, Lohmann TM. 1994. Single-turnover kinetics of helicase-catalyzed DNA unwinding monitored continuously by fluorescence energy transfer. Biochemistry 33:14306-14316.
6. Branch AD, Robertson HD. 1991. Efficient trans cleavage and a common structural motif for the ribozymes of the human hepatitis delta agent. Proc Natl Acad Sci USA 88:10163-10167.
7. Burke JM, Butcher SE, Sargueil B. 1996. Structural analysis and modifications of the hairpin ribozyme. In: Eckstein F, Lilley DMJ, eds. Nucleic acids and molecular biology, vol 10. Berlin: Springer-Verlag. pp 129-143.
8. Butcher SE, Heckman JE, Burke JM. 1995. Reconstitution of hairpin ribozyme activity following separation of functional domains. J Biol Chem 270:29648-29651.
9. Buzayan JM, Gerlach WL, Bruening G. 1986. Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA. Nature 323:349-353.
10. Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE. 1988. Detection of nucleic acid hybridization by nonradiative fluorescence energy transfer. Proc Natl Acad Sci USA 85:8790-8794.
11. Chowrira BM, Burke JM. 1991. Binding and cleavage of nucleic acids by the "hairpin" ribozyme. Biochemistry 30:8518-8522.
12. Clegg RM, Murchie AIH, Zechel A, Carlberg C, Diekmann S, Lilley DMJ. 1992. Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction. Biochemistry 31:4846-4856.
13. Cooper JP, Hagerman PJ. 1990. Analysis of fluorescence energy transfer in duplex and branched DNA molecules. Biochemistry 29:9261-9268.
14. Dapprich J, Walter NG, Salingue F, Staerk H. 1996. Base-dependent pyrene fluorescence used for in-solution detection of nucleic acids. In: Birch D, Miller J, eds. Special issue of J Fluorescence, Proceedings of the 4th International Conference on Methods and Applications of Fluorescence Spectroscopy. Forthcoming.
15. Fedor MJ, Uhlenbeck OC. 1992. Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry 31:12042-12054.
16. Feldstein PA, Buzayan JM, Bruening G. 1989. Two sequences participating in the autocatalyric processing of satellite tobacco ringspot virus complementary RNA. Gene 82:53-61.
17. Feldstein PA, Buzayan JM, van Tol H, de Bear J, Gough GR, Gilham PT, Bruening G. 1990. Specific association between an endoribonucleolytic sequence from a satellite RNA and a substrate analogue containing 2′-5′ phosphodiester. Proc Natl Acad Sci USA 87:2623-2627.
18. Forster AC, Symons RH. 1987. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49:211-220.
19. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-857.
20. Guo HCT, Collins RA. 1995. Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J 14:368-376.
21. Hampel A, Tritz R. 1989. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry 28:4929-4933.
22. Hampel A, Tritz R, Hicks M, Cruz P. 1990. "Hairpin" catalytic RNA model: Evidence for helices and sequence requirement for substrate RNA. Nucleic Acids Res 28:299-304.
23. Haseloff J, Gerlach WL. 1988. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334:585-591.
24. Hegg LA, Fedor MJ. 1995. Kinetics and thermodynamics of intermolecular catalysis by hairpin ribozymes. Biochemistry 34:15813-15828.
25. Herschlag D, Cech TR. 1990. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 2. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry 29:10159-10171.
26. Hiyoshi M, Hosoi S. 1994. Assay of DNA denaturation by polymerase chain reaction-driven fluorescent label incorporation and fluorescence resonance energy transfer. Anal Biochem 223:306-311.
27. Joseph S, Burke JM. 1993. Optimization of an anti-HIV hairpin ribozyme by in vitro selection. J Biol Chem 268:24515-24518.
28. Kierzek R, Li Y, Turner DH, Bevilacqua PC. 1993. 5′-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation. J Am Chem Soc 115: 4985-4992.
29. Kinjo M, Rigler R. 1995. Ultrasensitive hybridization analysis using fluorescence correlation spectroscopy. Nucleic Acids Res 23:1795-1799.
30. Koenig P, Reines SA, Cantor CR. 1977. Pyrene derivatives as fluorescent probes of conformation near the 3′ termini of polyribonucleotides. Biopolymers 16:2231-2242.
31. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrakymena. Cell 33:147-157.
32. Lakowicz JR. 1983. Principles of fluorescence spectroscopy. New York: • Plenum Press.
33. Lee SP, Porter D, Chirikjian JG, Knutson JR, Han MK. 1994. A fluorometric assay for DNA cleavage reactions characterized with BamHI restriction endonuclease. Anal Biochem 222:377-383.
34. Li Y, Bevilacqua PC, Matthews D, Turner DH. 1995. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: Docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry 34:14394-14399.
35. Lianos P, Georghiou S. 1979. Complex formation between pyrene and the nucleotides GMP, CMP, TMP and AMP. Photochem Photophys 29:13-21.
36. Livak KJ, Flood SJA, Marmara J, Giusti W, Deetz K. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Applic 4:357-362.
37. Manoharan M, Tivel KL, Zhao M, Nafisi K, Netzel TL. 1995. Base-sequence dependence of emission lifetimes for DNA oligomers and duplexes covalently labeled with pyrene: Relative electron-transfer quenching efficiencies of A, G, C, and T nucleoside toward pyrene. J Phys Chem 99:17461-17472.
38. Michels WJ Jr, Pyle AM. 1995. Conversion of a group II intron into a new multiple-turnover ribozyme that selectively cleaves oligonucleotides: Elucidation of reaction mechanism and structure/ function relationships. Biochemistry 34:2965-2977.
39. Morrison LE, Stols LM. 1993. Sensitive fluorescence-based thermo-dynamic and kinetic measurements of DNA hybridization in solution. Biochemistry 32:3095-3104.
40. Murchie AIH, Clegg RM, von Kitzing E, Duckett DR, Diekmann S, Lilley DMJ. 1989. Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules. Nature 343:763-766.
41. Parkhurst KM, Parkhurst LJ. 1995. Kinetic studies by fluorescence resonance energy transfer employing a double-labeled oligonucleotide: Hybridization to the oligonucleotide complement and to single-stranded DNA. Biochemistry 34:285-292.
42. Perkins TA, Wolf DE, Goodchild J. 1996. Fluorescence resonance energy transfer analysis of ribozyme kinetics reveals the mode of action of a facilitator oligonucleotide. Biochemistry 35:16370-16377.
43. Perrotta AT, Been MD. 1991. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature 350:434-436.
44. Porschke D, Uhlenbeck OC, Martin FH. 1973. Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs. Biopolymers 22:1313-1335.
45. Sargueil B, Pecchia DB, Burke JM. 1995. An improved version of the hairpin ribozyme functions as a ribonucleoprotein complex. Biochemistry 34:7739-7748.
46. Saville BJ, Collins RA. 1990. A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria. Cell 62:685-696.
47. Schwille P, Oehlenschläger F, Walter NG. 1996. Quantitative hybridization kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation analysis. Biochemistry 35:10182-10193.
48. Seidel CAM, Schulz A, Sauer MHM. 1996. Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J Phys Chem 100:5541-5553.
49. Shafirovich VY, Courtney SH, Ya N, Geacintov NE. 1995. Proton-coupled photoinduced electron transfer, deuterium isotope effects, and fluorescence quenching in noncovalent benzo[a]pyrenetetranol-nucleoside complexes in aqueous solutions. J Am Chem Soc 117:4920-4929.
50. Sharmeen L, Kuo MY, Dinter-Gottlieb G, Taylor J. 1988. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol 62:2674-2679.
51. Sproat B, Colonna F, Mullah B, Tsou D, Andrus A, Hample A, Vinayak R. 1995. An efficient method for isolation and purification of oligoribonucleotides. Nucleosides Nucleotides 14:255-273.
52. Sugimoto N, Sasaki M, Kierzek R, Turner DH. 1989. Binding of a fluorescent oligonucleotide to a circularized intervening sequence from Tetrahymena thermophila. Chem Lett:2223-2226.
53. Turner DH, Li Y, Fountain M, Profenno L, Bevilacqua PC. 1996. Dynamics of a group I ribozyme detected by spectroscopic methods. In: Eckstein F, Lilley DMJ, eds. Nucleic acids and molecular biology, vol 10. Berlin: Springer-Verlag, pp 19-32.
54. Tuschl T, Gohlke C, Jovin TM, Westhof E, Eckstein F. 1994. A threedimensional model for the hammerhead ribozyme based on fluorescence measurements. Science 266:785-789.
55. Tyagi S, Kramer FR. 1996. Molecular beacons: Probes that fluoresce upon hybridization. Nat Biotechnol 14:303-308.
56. Uhlenbeck OC. 1987. A small catalytic oligoribonucleotide. Nature 328:596-600.
57. Vinayak R, Andrus A, Sinha ND, Hampel A. 1995. Assay of ribozyme-substrate cleavage by anion-exchange high-performance liquid chromatography. Anal Biochem 232:204-209.
58. Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. 1994. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 91:9218-9222.
59. Yamana K, Gokota T, Ozaki H, Nakano H, Sangen O, Shimidzu T. 1992. Enhanced fluorescence in the binding of oligonucleotides with a pyrene group in the sugar fragment to complementary polynucleotides. Nucleosides Nucleotides 11:383-390.
60. Zaug AJ, Cech TR. 1986. The intervening sequence RNA of Tetrahymena is an enzyme. Science 231:470-475.