Hammerhead ribozymes designed to cleave all human rod opsin mRNAs which cause autosomal dominant retinitis pigmentosa

Molecular Vision

Volumn 8, Issue , 2002, Pages 102-113

  Sullivan, Jack M ^a   Pietras, Kathleen M ^a   Shin, Byant J ^a   Misasi, John N ^a  

^a State University of New York Upstate Medical University: College of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GUANINE; MESSENGER RNA; OPSIN; POLYACRYLAMIDE GEL; RIBOZYME; URACIL;

ALGORITHM; ARTICLE; AUTOSOMAL DOMINANT DISORDER; CELL SURVIVAL; CODON; CONTROLLED STUDY; ENZYME INHIBITION; ENZYME SUBSTRATE; GENE MUTATION; GENE THERAPY; GENETIC ENGINEERING; GENETIC TRANSCRIPTION; HUMAN; IN VITRO STUDY; PHOTORECEPTOR; POLYACRYLAMIDE GEL ELECTROPHORESIS; RETINA ROD; RETINITIS PIGMENTOSA; RNA DEGRADATION; RNA STRUCTURE;

BASE SEQUENCE; DRUG DESIGN; ELECTROPHORESIS, POLYACRYLAMIDE GEL; FORMAMIDES; GENE EXPRESSION; HEAT; HUMANS; IMMUNOHISTOCHEMISTRY; MOLECULAR SEQUENCE DATA; OPSIN; PLASMIDS; POLYMERASE CHAIN REACTION; RETINITIS PIGMENTOSA; RNA; RNA, CATALYTIC; RNA, MESSENGER; RODS (RETINA); TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 0036974435     PISSN: 10900535     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (83)

1. Haseloff J, Gerlach WL. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 1988; 334:585-91.
2. Herschlag D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc Natl Acad Sci U S A 1991; 88:6921-5.
3. Hertel KJ, Peracchi A, Uhlenbeck OC, Herschlag D. Use of intrinsic binding energy for catalysis by an RNA enzyme. Proc Natl Acad Sci U S A 1997; 94:8497-502.
4. Drenser KA, Timmers AM, Hauswirth WW, Lewin AS. Ribozyme-targeted destruction of RNA associated with autosomal-dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 1998; 39:681-9.
5. Lewin AS, Drenser KA, Hauswirth WW, Nishikawa S, Yasamura D, Flannery JG, LaVail MM. Ribozyme rescue of photoreceptor cells in transgenic rat model of autosomal dominant retinitis pigmentosa. Nat Med 1998; 4:967-71.
6. Shimayama T, Nishikawa S, Taira K. Generality of the NUX rule: kinetic analysis of the results of systematic mutations in the trinucleotide at the cleavage site of hammerhead ribozymes. Biochemistry 1995; 34:3649-54.
7. Zoumadakis M, Tabler M. Comparative analysis of cleavage rates after systematic permutation of the NUX consensus target motif for hammerhead ribozymes. Nucleic Acids Res 1995; 23:1192-6.
8. Koizumi M, Hayase Y, Iwai S, Kamiya H, Inoue H, Ohtsuka E. Design of RNA enzymes distinguishing a single base mutation in RNA. Nucleic Acids Res 1989; 17:7059-71.
9. Werner M, Uhlenbeck OC. The effect of base mismatches in the substrate recognition helices of hammerhead ribozymes on binding and catalysis. Nucleic Acids Res 1995; 23:2092-6.
10. Gal A, Apfelstedt-Sylla E, Janecke AR, Zrenner E. Rhodopsin mutations in inherited retinal dystrophies and dysfunctions. Prog Retin Eye Res 1997; 16:51-79.
11. Sandberg MA, Weigel-DiFranco C, Dryja TP, Berson EL. Clinical expression correlates with location of rhodopsin mutation in dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 1995; 36:1934-42.
12. Sung CH, Schneider BG, Agarwal N, Papermaster DS, Nathans J. Functional heterogeneity of mutant rhodopsins responsible for autosomal dominant retinitis pigmentosa. Proc Natl Acad Sci U S A 1991; 88:8840-4.
13. Fain GL, Lisman JE. Photoreceptor degeneration in vitamin A deprivation and retinitis pigmentosa: the equivalent light hypothesis. Exp Eye Res 1993; 57:335-40.
14. Colley NJ, Cassill JA, Baker EK, Zuker CS. Defective intracellular transport is the molecular basis of rhodopsin-dependent dominant retinal degeneration. Proc Natl Acad Sci U S A 1995; 92:3070-4.
15. Frederick JM, Krasnoperova NV, Hoffmann K, Church-Kopish J, Ruther K, Howes K, Lem J, Baehr W. Mutant rhodopsin transgene expression on a null background. Invest Ophthalmol Vis Sci 2001; 42:826-33.
16. Chang GQ, Hao Y, Wong F. Apoptosis: final common pathway of photoreceptor death in rd, rds, and rhodopsin mutant mice. Neuron 1993; 11:595-605.
17. Portera-Cailliau C, Sung CH, Nathans J, Adler R. Apoptotic photoreceptor cell death in mouse models of retinitis pigmentosa. Proc Natl Acad Sci U S A 1994; 91:974-8.
18. Kraft TW, Schneeweis DM, Schnapf JL. Visual transduction in human rod photoreceptors. J Physiol 1993; 464:747-65.
19. Rosenfeld PJ, Cowley GS, McGee TL, Sandberg MA, Berson EL, Dryja TP. A null mutation in the rhodopsin gene causes rod photoreceptor dysfunction and autosomal recessive retinitis pigmentosa. Nat Genet 1992; 1:209-13.
20. Rosenfeld PJ, Hahn LB, Sandberg MA, Dryja TP, Berson EL. Low incidence of retinitis pigmentosa among heterozygous carriers of a specific rhodopsin splice mutation. Invest Ophthal Vis Sci 1995; 36:2186-92.
21. Humphries MM, Rancourt D, Farrar GJ, Kenna P, Hazel M, Bush RA, Sieving PA, Sheils DM, McNally N, Creighton P, Erven A, Boros A, Gulya K, Capecchi MR, Humphries P. Retinopathy induced in mice by targeted disruption of the rhodopsin gene. Nat Genet 1997; 15:216-9.
22. Penn JS, Williams TP. Photostasis: regulation of daily photon-catch by rat retinas in response to various cyclic illuminances. Exp Eye Res 1986; 43:915-28.
23. Montgomery RA, Dietz HC. Inhibition of fibrillin 1 expression using U1 snRNA as a vehicle for the presentation of antisense targeting sequence. Hum Mol Genet 1997; 6:519-25.
24. Millington-Ward S, O'Neill B, Tuohy G, Al-Jandal N, Kiang AS, Kenna PF, Palfi A, Hayden P, Mansergh F, Kennan A, Humphries P, Farrar GJ. Strategems in vitro for gene therapies directed to dominant mutations. Hum Mol Genet 1997; 6:1415-26.
25. Sullivan JM, Pietras KM, Shin BJ. Design and testing of hammerhead ribozymes to cleave full-length opsin mRNA. Invest Ophthalmol Vis Sci 1998; 39:S722.
26. Ozaki I, Zern MA, Liu S, Wei DL, Pomerantz RJ, Duan L. Ribozyme-mediated specific gene replacement of the alpha 1-antitrypsin gene in human hepatoma cells. J Hepatol 1999; 31:53-60.
27. Taylor NR, Rossi JJ. Ribozyme-mediated cleavage of an HIV-1 gag RNA: the effects of nontargeted sequences and secondary structure on ribozyme cleavage activity. Antisense Res Dev 1991; 1:173-86.
28. Xing, Z, Whitton JL. Ribozymes which cleave arenavirus RNAs: identification of susceptible target sites and inhibition by target site secondary structure. J Virol 1992; 66:1361-9.
29. Scarabino D, Tocchini-Valentini GP. Influence of substrate structure on cleavage by hammerhead ribozyme. FEBS Lett 1996; 383:185-90.
30. Ho SP, Britton DH, Stone BA, Behrens DL, Leffet LM, Hobbs FW, Miller JA, Trainor GL. Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Res 1996; 24:1901-7.
31. Birikh KR, Berlin YA, Soreq H, Eckstein F. Probing accessible sites for ribozymes on human acetylcholinesterase RNA. RNA 1997; 3:429-37.
32. Campbell TB, McDonald CK, Hagen M. The effect of structure in a long target RNA on ribozyme cleavage efficiency. Nucleic Acids Res 1997; 25:4985-93.
33. Milner N, Mir KU, Southern EM. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 1997; 15:537-41.
34. Ho SP, Bao Y, Lesher T, Malhotra R, Ma LY, Fluharty SJ, Sakai RR. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat Biotechnol 1998; 16:59-63.
35. Yu Q, Pecchia DB, Kingsley SL, Heckman JE, Burke JM. Cleavage of highly structured viral RNA molecules by combinatorial libraries of hairpin ribozymes. The most effective ribozymes are not predicted by substrate selection rules. J Biol Chem 1998; 273:23524-33.
36. Scherr M, Rossi JJ. Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts. Nucleic Acids Res 1998; 26:5079-85.
37. zu Putlitz J, Yu Q, Burke JM, Wands JR. Combinatorial screening and intracellular antiviral activity of hairpin ribozymes directed against hepatitis B virus. J Virol 1999; 73:5381-7.
38. Vickers TA, Wyatt JR, Freier SM. Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res 2000; 28:1340-7.
39. Rittner K, Burmester C, Sczakiel G. In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1. Nucleic Acids Res 1993; 21:1381-7.
40. Patzel V, Sczakiel G. Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat Biotechnol 1998; 16:64-8.
41. Richards JE, Scott KM, Sieving PA. Disruption of conserved rhodopsin disulfide bond by Cys187Tyr mutation causes early and severe autosomal dominant retinitis pigmentosa. Ophthalmology 1995; 102:669-77.
42. Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 1984; 12:387-95.
43. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res 1981; 9:133-48.
44. Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A 1989; 86:7706-10.
45. Ruffner DE, Stormo GD, Uhlenbeck OC. Sequence requirements of the hammerhead RNA self-cleavage reaction. Biochemistry 1990; 29:10695-702.
46. Nathans J, Hogness DS. Isolation and nucleotide sequence of the gene encoding human rhodopsin. Proc Natl Acad Sci U S A 1984; 81:3851-5.
47. Deng WP, Nickoloff JA. Site-directed mutagenesis of virtually any plasmid by eliminating a unique site. Anal Biochem 1992; 200:81-8.
48. Sullivan JM, Satchwell MF. Development of stable cell lines expressing high levels of point mutants of human opsin for biochemical and biophysical studies. Methods Enzymol 2000; 315:30-58.
49. Homann M, Tabler M, Tzortzakaki S, Sczakiel G. Extension of helix II of an HIV-1-directed hammerhead ribozyme with long antisense flanks does not alter kinetic parameters in vitro but causes loss of the inhibitory potential in living cells. Nucleic Acids Res 1994; 22:3951-7.
50. Pokrovskaya ID, Gurevich VV. In vitro transcription: preparative RNA yields in analytical scale reactions. Anal Biochem 1994; 220:420-3.
51. Fedor MJ, Uhlenbeck OC. Substrate sequence effects on "hammerhead" RNA catalytic efficiency. Proc Natl Acad Sci U S A 1990; 87:1668-72.
52. Fedor MJ, Uhlenbeck OC. Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry 1992; 31:12042-54.
53. Walstrum SA, Uhlenbeck OC. The self-splicing RNA of Tetrahymena is trapped in a less active conformation by gel purification. Biochemistry 1990; 29:10573-6.
54. Stillman BW, Gluzman Y. Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells. Mol Cell Biol 1985; 5:2051-60.
55. Stull RA, Taylor LA, Szoka FC Jr. Predicting antisense oligonucleotide inhibitory efficacy: a computational approach using histograms and thermodynamic indices. Nucleic Acids Res 1992; 20:3501-8.
56. Sczakiel G, Homann M, Rittner K. Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1. Antisense Res Dev 1993; 3:45-52.
57. Sczakiel G, Tabler M. Computer-aided calculation of the local folding potential of target RNA and its use for ribozyme design. In: Turner PC, editor. Methods in molecular biology. Ribozyme protocols, vol 74. Totowa (NJ): Humana Press; 1997. p 11-15.
58. James W, Cowe E. Computational approaches to the identification of ribozyme target sites. In: Turner PC, editor. Methods in molecular biology. Ribozyme protocols, vol 74. Totowa (NJ): Humana Press; 1997. p 17-26.
59. Matveeva O, Felden B, Audlin S, Gesteland RF, Atkins JF. A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures. Nucleic Acids Res 1997; 25:5010-6.
60. Patzel V, Steidl U, Kronenwett R, Haas R, Sczakiel G. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. Nucleic Acids Res 1999; 27:4328-34.
61. Scherr M, Rossi JJ, Sczakiel G, Patzel V. RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. Nucleic Acids Res 2000; 28:2455-61.
62. Scherr M, Reed M, Huang CF, Riggs AD, Rossi JJ. Oligonucleotide scanning of native mRNAs in extracts predicts intracellular ribozyme efficiency: ribozyme-mediated reduction of the murine DNA methyltransferase. Mol Ther 2000; 2:26-38.
63. Amarzguioui M, Brede G, Babaie E, Grotli M, Sproat B, Prydz H. Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes. Nucleic Acids Res 2000; 28:4113-24.
64. Ding Y, Lawrence CE. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense targets sites and beyond. Nucleic Acids Res 2001; 29:1034-46.
65. Christoffersen RE, McSwiggen JM, Konings D. Application of computational technologies to ribozyme biotechnology products. J Mol Struct 1994; 311:272-84.
66. Palfner K, Kneba M, Hiddemann W, Bertram J. Improvement of hammerhead ribozymes cleaving mdr-1 mRNA. Biol Chem Hoppe Seyler 1995; 376:289-95.
67. Long DM, Uhlenbeck OC. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. Proc Natl Acad Sci U S A 1994; 91:6977-81.
68. Heidenreich O, Eckstein F. Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type I. J Biol Chem 1992; 267:1904-9.
69. Ellis J, Rogers J. Design and specificity of hammerhead ribozymes against calretinin mRNA. Nucleic Acids Res 1993; 21:5171-8.
70. Hendrix C, Anne J, Joris B, Van Aerschot A, Herdewijn P. Selection of hammerhead ribozymes for optimum cleavage of interleukin 6 mRNA. Biochem J 1996; 314:655-61.
71. Stage-Zimmermann TK, Uhlenbeck OC. Hammerhead ribozyme kinetics. RNA 1998; 4:875-89.
72. Kisich KO, Freedland SJ, Erickson KL. Factors altering ribozyme-mediated cleavage of tumor necrosis factor-alpha mRNA in vitro. Biochem Biophys Res Commun 1997; 236:205-11.
73. Woisard A, Fourrey JL, Favre A. Multiple folded conformations of a hammerhead ribozyme domain under cleavage conditions. J Mol Biol 1994; 239:366-70.
74. Simorre JP, Legault P, Baidya N, Uhlenbeck OC, Maloney L, Wincott F, Usman N, Beigelman L, Pardi A. Structural variation induced by different nucleotides at the cleavage site of the hammerhead ribozyme. Biochemistry 1998; 37:4034-44.
75. Karnik SS, Khorana HG. Assembly of functional rhodopsin requires a disulfide bond between cysteine residues 110 and 187. J Biol Chem 1990; 265:17520-4.
76. Korenbrot JI, Fernald RD. Circadian rhythm and light regulate opsin mRNA in rod photoreceptors. Nature 1989; 337:454-7.
77. McGinnis JF, Whelan JP, Donoso LA. Transient, cyclic changes in mouse visual cell gene products during light-dark cycle. J Neurosci Res 1992; 31:584-90.
78. Herschlag D, Khosla M, Tsuchihashi Z, Karpel RL. An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J 1994; 13:2913-24.
79. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999; 288:911-40.
80. Herschlag D. RNA chaperones and the RNA folding problem. J Biol Chem 1995; 270:20871-4.
81. McInnes RR, Bascom RA. Retinal genetics: a nullifying effect for rhodopsin. Nat Genet 1992; 1:155-7.
82. O'Neill B, Millington-Ward S, O'Reilly M, Tuoby G, Kiang AS, Kenna PF, Humphries P, Farrar GJ. Ribozyme-based therapeutic approaches for autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 2000; 41:2863-9.
83. Beck J, Nassal M. Efficient hammerhead ribozyme-mediated cleavage of the structured hepatitis B virus encapsidation signal in vitro and in cell extracts, but not in intact cells. Nucleic Acids Res 1995; 23:4954-62.