In vitro selection of a novel nuclease-resistant RNA phosphodiesterase

Chemistry and Biology

Volumn 7, Issue 5, 2000, Pages 323-334

  Beaudry, Amber ^a   Defoe, James ^a   Zinnen, Shawn ^a   Burgin, Alex ^b   Beigelman, Leonid ^a  

^a Sirna Therapeutics Inc   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

2' deoxy 2' aminopyrimidine RNA; Catalytic RNA; In vitro selection; Ribozymes; RNA therapeutics

Indexed keywords

ANIMALIA;

EID: 0034069921     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(00)00110-1     Document Type: Article

References (63)

1. Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E., Cech T.R. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence. Cell. 31:1982;147-157.
2. Guerrier-Takada C., Gardiner K., Marsh T., Pace N., Altman S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 35:1983;849-857.
3. Christoffersen R.E., Marr J.J. Ribozymes as human therapeutic agents. J. Med. Chem. 38:1995;2024-2037.
4. Beigelman L., Usman N.et al. Chemical modification of hammerhead ribozymes. J. Biol. Chem. 43:1995;25702-25708.
5. Paolella G., Sproat B.S., Lamond A.I. Nuclease resistant ribozyme with high catalytic activity. EMBO J. 11:1992;1913-1919.
6. Flory C.M., Schrier D.J.et al. Nuclease-resistant ribozymes decrease stromelysin mRNA levels in rabbit synovium following exogenous deliver to the knee joint. Proc. Natl Acad. Sci. USA. 93:1996;754-758.
7. Jarvis T.C., Stinchcomb D.T.et al. Inhibition of vascular smooth muscle cell proliferation by ribozymes that cleave c-myb mRNA. RNA. 2:1996;419-428.
8. Parry J.T., Pavco P.E.et al. Bioactivity of anti-angiogenic ribozymes targeting Flt-1 and KDR mRNA. Nucleic Acids Res. 27:1999;2569-2577.
9. Sioud M., Sorenson D.R. A nuclease-resistant protein kinase C α ribozyme blocks glioma cell growth. Nat. Biotechnol. 16:1998;556-561.
10. Pyle A.M. Ribozymes: a distinct class of metalloenzymes. Science. 261:1993;709-714.
11. Eckstein F., Lilley D.M.J Catalytic RNA (2nd edn). 1997;Springer, Berlin.
12. Sigurdsson S.T., Thomson J.B., Eckstein F. Small Ribozymes. Simons R.W., Grunberg-Manago M. In RNA Structure and Function. 1998;339-376 Cold Spring Harbor Laboratory Press, New York.
13. Breaker R.R. In vitro selection of catalytic polynucleotides. Chem. Rev. 98:1998;2260-2290.
14. Pan T. Novel and variant ribozymes obtained through in vitro selection. Curr. Opin. Chem. Biol. 1:1997;17-25.
15. Lorsch J.R., Szostak J.W. Chance and necessity in the selection of nucleic acid catalysts. Accounts Chem. Res. 29:1996;103-110.
16. Joyce G.F. In vitro evolution of nucleic acids. Curr. Opin. Struct. Biol. 4:1994;331-336.
17. Joyce G.F. Amplification, mutation and selection of catalytic RNA. Gene. 82:1989;83-87.
18. Tuerk C., Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249:1990;505-510.
19. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
20. 2+ dependent self-cleaving ribozymes. EMBO J. 14:1995;4551-4557.
21. Long D.M., Uhlenbeck O. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions. Proc. Natl Acad. Sci. USA. 91:1994;6977-6981.
22. Ishizaka M., Ohshima Y., Tani T. Isolation of active ribozymes from an RNA pool of random sequences using an anchored substrate RNA. Biochem. Biophys. Res. Comm. 214:1995;403-409.
23. Nakamaye K.L., Eckstein F. AUA-cleaving hammerhead ribozymes: attempted selection for improved cleavage. Biochemistry. 33:1994;1271-1277.
24. Thomson J.B., Sigurdsson S.T., Zeuch A., Eckstein F. In vitro selection of hammerhead ribozymes containing a bulged nucleotide in stem II. Nucleic Acids Res. 24:1996;4401-4406.
25. Vaish N.K., Heaton P.A., Eckstein F. Isolation of hammerhead ribozymes with altered core sequences by in vitro selection. Biochemistry. 36:1997;6495-6501.
26. 2+ concentration. Nucleic Acids Res. 27:1999;2400-2407.
27. Zillmann M., Limauro S.E., Goodchild J. In vitro optimization of truncated stem-loop II variants of the hammerhead ribozyme for cleavage in low concentrations of magnesium under non-turnover conditions. RNA. 3:1997;734-747.
28. Burgin A.B., Beigelman L.et al. Chemically modified hammerhead ribozymes with improved catalytic rates. Biochemistry. 35:1996;14090-14097.
29. Vaish N., Heaton P., Fedorova O., Eckstein F. In vitro selection of a purine nucleotide-specific hammerhead-like ribozyme. Proc. Natl Acad. Sci. USA. 95:1998;2158-2162.
30. Chartrand P., Harvey S., Ferbeyre G., Usman N., Cedergren R. An oligodeoxyribonucleotide that supports catalytic activity in the hammerhead ribozyme domain. Nucleic Acid Res. 23:1995;4092-4096.
31. Breaker R., Joyce G. A DNA enzyme that cleaves RNA. Chem. Biol. 1:1994;223-229.
32. 2+-dependent RNA phosphoesterase activity. Chem. Biol. 2:1995;655-660.
33. Santoro S., Joyce G. A general purpose RNA-cleaving DNA enzyme. Proc. Natl Acad. Sci. USA. 94:1997;4262-4266.
34. Santoro S., Joyce G. Mechanism and utility of an RNA-cleaving DNA enzyme. Biochemistry. 37:1998;13330-13342.
35. Warashina M., Kuwabara T., Nakamatsu Y., Taira K. Extremely high and specific activity of DNA enzymes in cells with a Philadelphia chromosome. Chem. Biol. 6:1999;237-250.
36. Cairns M., Hopkins T., Witherington C., Wang L., Sun L. Target site selection for an RNA-cleaving catalytic DNA. Nat. Biotechnol. 17:1999;480-486.
37. Sun L., Cairns M., Gerlach W., Witherington C., Wang L., King A. Suppression of smooth muscle cell proliferation by a c-myc RNA-cleaving deoxyribozyme. J. Biol. Chem. 274:1999;17236-17241.
38. 2+ and deoxynucleoside monophosphate incorporation into transcripts. Biochemistry. 36:1997;13718-13728.
39. Lin Y., Qiu Q., Gill S., Jayasena S. Modified RNA sequence pools for in vitro selection. Nucleic Acids Res. 22:1994;5229-5234.
40. Freier S.M., Turner D.H.et al. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA. 83:1986;9373-9377.
41. Aurup H., Tuschl T., Benseler F., Ludwig J., Eckstein F. Oligonucleotide duplexes containing 2′-amino-2′-deoxycytidines: thermal stability and chemical reactivity. Nucleic Acids Res. 22:1994;20-24.
42. Vartanian J., Henry M., Wain-Hobson S. Hypermutagenic PCR involving all four transitions and a sizeable proportion of transversions. Nucleic Acids Res. 24:1996;2627-2631.
43. Dahm S., Derrick W., Uhlenbeck O. Evidence for the role of solvated metal hydroxide in hammerhead cleavage mechanism. Biochemistry. 32:1993;13040-13045.
44. Hertel K., Herschlag D., Uhlenbeck O. A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry. 33:1994;3374-3385.
45. Murray J., Seyhan A., Walter N., Burke J., Scott W. The hammerhead, hairpin, and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5:1998;587-595.
46. Zucker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
47. Ferre-D'Amare A.R., Zhou K., Doudna J.A. Crystal structure of a hepatitus delta virus ribozyme. Nature. 395:1998;567-574.
48. Perrotta A.T., I-hung S., Been M.D. Imidazole rescue of cytosine mutation in a self-cleaving ribozyme. Science. 286:1999;123-126.
49. Agrawal S., Temsamani J., Galbraith W., Tang J. Y Pharmacokineticis of antisence oligonucleotides. Clin. Pharmacokinet. 28:1995;7-16.
50. TM) in the mouse. Antisense Nucl. Acid Drug Dev. 9:1999;271-277.
51. Narlikar G.J., Herschlag D. Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes. Ann. Rev. Biochem. 66:1997;19-59.
52. Tarasow T.M., Eaton B.E. Dresses for success: realizing the catalytic potential of RNA. Biopolymers. 48:1998;29-37.
53. Wiegand T.W., Janssen R.C., Eaton B.E. Selection of RNA amide synthases. Chem. Biol. 4:1997;675-683.
54. Tarasow T.M., Tarasow S.L., Eaton B.E. RNA-catalysed carbon-carbon bond formation. Nature. 389:1997;54-57.
55. Morris K.N., Gold L.et al. Enrichment for RNA molecules that bind a Diels-Alder transition state analog. Proc. Natl Acad. Sci. USA. 91:1994;13028-13032.
56. Sakthivel K., Barbas C.F. III Expanding the potential of DNA for binding and catalysis: highly functionalized dUTP derivatives that are substrates for thermostable DNA polymerases. Angew. Chem. Int. Ed. 37:1998;2872-2875.
57. Perrin D.M., Garestier T., Helene C. Expanding the catalytic repertoire of nucleic acid catalysts: simultaneous incorporation of two modified deoxyribonucleoside triphosphates bearing ammonium and imidazolyl functionalities. Nucleosides Nucleotides. 18:1999;377-391.
58. Herschlag D., Jencks W.P. Phosphoryl transfer to anionic oxygen nucleophiles. Nature of the transition state and electrostatic repulsion. J. Am. Chem. Soc. 111:1989;7587-7596.
59. Herschlag D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270:1995;20871-20874.
60. Roth A., Breaker R.R. An amino acid as a cofactor for a catalytic polynucleotide. Proc. Natl Acad. Sci. USA. 95:1998;6027-6031.
61. Joyce G.F. Nucleic acid enzymes: playing with a fuller deck. Proc. Natl Acad. Sci. USA. 95:1998;5845-5847.
62. Pyle A., McSwiggen J., Cech T. Direct measurement of oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena. Biochemistry. 87:1990;8187-8191.
63. Fedor M., Uhlenbeck O. Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry. 31:1992;12042-12054.