Selecting optimal antisense reagents

Advanced Drug Delivery Reviews

Volumn 44, Issue 1, 2000, Pages 23-34

  Sohail, M ^a   Southern, E M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Antisense oligonucleotides; Deoxyribozymes; Oligonucleotide scanning arrays; Ribozymes; RNase H mapping; RNase T1; Secondary structure; Target selection

Indexed keywords

AGENTS; DRUG PRODUCTS; ENZYME KINETICS; RNA;

ANTISENSE REAGENTS; OLIGONUCLEOTIDE SCANNING ARRAYS;

CONTROLLED DRUG DELIVERY;

ANTISENSE OLIGONUCLEOTIDE; ANTISENSE REAGENT; HETERODUPLEX; NUCLEIC ACID; REAGENT; RIBONUCLEASE H; RIBONUCLEASE T1; RIBOZYME; RNA; UNCLASSIFIED DRUG;

BASE PAIRING; COMPUTER AIDED DESIGN; DNA FOOTPRINTING; DNA MICROARRAY; GENE LIBRARY; GENE MAPPING; GENE TARGETING; GENE THERAPY; NUCLEIC ACID HYBRIDIZATION; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE;

EID: 0034739611     PISSN: 0169409X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-409X(00)00081-8     Document Type: Article

References (64)

1. Milner N., Mir K.U., Southern E.M. Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat. Biotechnol. 15:1997;537-541.
2. Southern E.M., Case-Green S.C., Elder J.K., Johnson M., Mir K.U., Wang L., Williams J.C. Arrays of complementary oligonucleotides for analysing the hybridisation behaviour of nucleic acids. Nucleic Acids Res. 22:1994;1368-1373.
3. Frauendorf A., Engels J.W. Interaction of linear and folded modified antisense oligonucleotides with sequences containing secondary structure elements. Bioorg. Med. Chem. Lett. 4:1996;1019-1024.
4. Wegner R.W., Matteucci M.D., Grant D., Huang T., Froehler B.C. Potent and selective inhibition of gene expression by an antisense heptanucleotide. Nat. Biotechnol. 14:1996;840-844.
5. Birikh K.R., Berlin Y.A., Soreq H., Eckstein F. Probing accessible sites for ribozymes on human acetylcholinesterase RNA. RNA. 3:1997;429-437.
6. Eckstein F. Searching for the ideal partner. Nat. Biotechnol. 16:1998;24.
7. Ho S.P., Bao Y., Lesher T., Malhotra R., Ma L.Y., Fluharty S.J., Sakai R.R. Mapping of RNA accessible sites for antisense experiments with oligonucleotide libraries. Nat. Biotechnol. 16:1998;59-63.
8. Patzel V., Sczakiel G. Theoretical design of antisense RNA structure substantially improves annealing kinetics and efficacy in human cells. Nat. Biotechnol. 16:1998;64-68.
9. Sohail M., Akhtar S., Southern E.M. The folding of large RNAs studied by hybridisation to arrays of complementary oligonucleotides. RNA. 5:1999;646-655.
10. Schwille P., Oehlenschlager F., Walter N.G. Quantitative hybridisation kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation analysis. Biochemistry. 35:1996;10182-10193.
11. Kozak M. Structural features in eukaryotic mRNAs that modulate the initiation of translation. J. Biol. Chem. 266:1991;19867-19870.
12. Kozak M. Features in the 5′ Non-coding sequences of rabbit α- and β-globin mRNAs that affect translational efficiency. J. Mol. Biol. 235:1994;95-110.
13. Storey A., Oates D., Banks L., Crawford L., Crook T. Anti-sense phosphorothioate oligonucleotides have both specific and non-specific effects on cells containing human papillomavirus type 16. Nucleic Acids Res. 19:1991;4109-4114.
14. Bacon T.A., Wickstrom E. Walking along the human c-myc mRNA with antisense oligodeoxynucleotides: maximum efficacy at the 5′ cap region. Oncogene Res. 6:1991;13-19.
15. Proudfoot N. Ending the message is not so simple. Cell. 87:1996;779-781.
16. Tu G.-C., Cao Q.-N., Zhou F., Israel Y. Tetranucleotide GGGA motif in primary RNA transcripts: Novel target site for antisense design. J. Biol. Chem. 273:1998;25125-25131.
17. Smetsers T.F.C.M., Boezeman J.B.M., Mensink E.J.B.M. Bias in nucleotide composition of antisense oligonucleotides. Antisense Nucleic Acids Drug Dev. 6:1996;63-67.
18. Cairns M.J., Hopkins T.M., Witherington C., Wang L., Sun L.-Q. Target site selection for an RNA-cleaving catalytic DNA. Nat. Biotechnol. 17:1999;480-486.
19. Peyman A., Helsberg M., Kretzschmar G., Mag M., Grabley S., Uhlmann E. Inhibition of viral growth by antisense oligonucleotides directed against the IE110 and the UL30 mRNA of Herpes Simplex Virus Type-1. Biol. Chem. Hoppe-Seyler. 376:1995;195-198.
20. Monia B.P., Johnston J.F., Geiger T., Muller M., Fabbro D. Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase. Nat. Med. 2:1996;668-675.
21. Stull R.A., Zon G., Szoka F.C. Jr. An in vitro messenger RNA binding assay as a tool for identifying hybridisation-competent antisense oligonucletoides. Antisense Nucleic Acid Drug Dev. 6:1996;221-228.
22. Minshull J., Hunt T. The use of single-stranded DNA and RNase H to promote quantitative 'hybrid arrest of translation' of mRNA/DNA hybrids in reticulocyte lysate cell-free translations. Nucleic Acids Res. 14:1986;6433-6451.
23. Chen T.-Z., Lin S.-B., Wu J.-C., Choo K.-B., Au L.-C. A method for screening antisense oligodeoxyribonucleotides effective for mRNA translation-arrest. J. Biochem. 119:1996;252-255.
24. dHellencourt C.L., Diaw L., Cornillet P., Guenounou M. Inhibition of human TNF alpha and LT in cell-free extracts and in cell culture by antisense oligonucleotides. Biochim. Biophys. Acta. 1317:1996;168-174.
25. Taylor M.F., Paulauskis J.D., Weller D.D., Kobzik L. In vitro efficacy of morpholino-modified antisense oligomers directed against tumor necrosis factor alpha mRNA. J. Biol. Chem. 271:1996;17445-17452.
26. Alt M., Renz R., Hofschneider P.H., Caselmann W.H. Core specific antisense phosphorothioate oligodeoxynucleotides as potent and specific inhibitors of hepatitis C viral translation. Arch. Virol. 142:1997;589-599.
27. Gee J.E., Robbins I., VanderLaan A.C., VanBoom J.H., Colombier C., Leng M., Raible A.M., Nelson J.S., Lebleu B. Assessment of high-affinity hybridisation, RNase H cleavage, and covalent linkage in translation arrest by antisense oligonucleotides. Antisense Nucleic Acid Drug Dev. 8:1998;103-111.
28. Scherr M., Rossi J.J. Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts. Nucleic Acids Res. 26:1998;5079-5085.
29. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
30. Lima W.F., Monia B.P., Ecker D.J., Freier S.M. Implication of RNA structure on antisense oligonucleotide hybridisation kinetics. Biochemistry. 31:1992;12055-12061.
31. Thierry A.R., Rahman A., Dritschilo A. Overcoming multidrug resistance in human tumor cells using free and liposomally encapsulated antisense oligodeoxynucleotides. Biochem. Biophys. Res. Commun. 190:1993;952-960.
32. Laptev A.V., Lu Z., Colige A., Prockop D.J. Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA. Biochemistry. 33:1994;11033-11039.
33. Michel F., Westhof E. Modelling of the three-dimensional architecture of Group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
34. Gaspin C., Westhof E. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol. 254:1995;163-174.
35. Eguchi Y., Itoh T., Tomizawa J.-I. Antisense RNA. Annu. Rev. Biochem. 60:1991;631-652.
36. Toulme J.J., Tinevez R.L., Brossalina E. Targeting RNA structure by antisense oligonucleotides. Biochemie. 78:1996;663673.
37. Southern E.M., Milner N., Mir K.U. Discovering antisense reagents by hybridisation of RNA to oligonucleotide arrays. Chadwick D.J., Cardew G. Oligonucleotides as Therapeutic Agents. Ciba Foundation Symposium 209. 1997;38-46 Wiley, Chichester.
38. Southern E.M., Mir K., Shchepinov M. Molecular interactions on microarrays. Nat. Med. Supl. 21:1999;5-9.
39. Kim S.H., Suddath F.L., Quigley G.J., McPherson A., Sussman J.L., Wang A.H.J., Seeman N.C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 185:1974;435-440.
40. Robertus J.D., Ladner J.E., Finch J.T., Rhodes D., Brown R.S., Clark B.F.C., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 250:1974;546-551.
41. K.U. Mir, Novel approaches for the analysis of nucleic acids, D. Phil. Thesis, University of Oxford, Oxford, 1995.
42. J.K. Elder, M. Johnson, N. Milner, K.U. Mir, M. Sohail, E.M. Southern, Antisense oligonucleotide scanning arrays, in: M. Schena (Ed.), DNA Microarrays: a Practical Approach, IRL Press, Oxford, 1999, 77-99.
43. Maskos U., Southern E.M. Oligonucleotide hybridisations on glass supports: a novel linker for oligonucleotide synthesis and hybridisation properties of oligonucleotides synthesised in situ. Nucleic Acids Res. 20:1992;1679-1684.
44. Matson R.S., Rampal J.B., Coassin P.J. Biopolymer synthesis on polypropylene supports: I. Oligonucleotides. Anal. Biochem. 217:1994;306-310.
45. Bertrand E.L., Rossi J.J. Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of hiv-1 and the heterogeneous nuclear ribonucleoprotein A1. EMBO J. 13:1994;2904-2912.
46. Herschlag D., Khosla M., Tsuchihashi Z., Karpel R.L. An RNA chaperone activity of nonspecific RNA-binding proteins in hammerhead ribozyme catalysis. EMBO J. 13:1994;2913-2924.
47. Tsuchihashi Z., Khosla M., Herschlag D. Protein enhancement of hammerhead ribozyme catalysis. Science. 262:1993;99-102.
48. Donis-Keller H. Site specific enzymatic cleavage of RNA. Nucleic Acids Res. 7:1979;179-192.
49. Wagner R.W., Matteucci M.D., Grant D., Huang T., Froehler B.C. Potent and selective inhibition of gene expression by an antisense heptanucleotide. Nature Biotechnol. 14:1996;840-844.
50. Woolf T.M., Melton D.A., Jennings C.G.B. Specificity of antisense oligonucleotides in vivo. Proc. Natl. Acad. Sci. USA. 89:1992;7305-7309.
51. Ho S.P., Britton D.H.O., Stone B.A., Behrens D.L., Leffet L.M., Hobbs F.W., Miller J.A., Trainor G.L. Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries. Nucleic Acids Res. 24:1996;1901-1907.
52. Lima W.F., Brown-Driver V., Fox M., Hanecak R., Bruice T. Combinatorial screening and rational optimization for hybridisation to folded Hepatitis C virus RNA of oligonucleotides with biological antisense activity. J. Biol. Chem. 272:1997;626-638.
53. Inoue H., Hayase Y., Iwai S., Ohtsuka E. Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H. FEBS Lett. 215:1987;327-330.
54. Hayase Y., Inoue H., Ohtsuka E. Secondary structure in Formylmethionine tRNA influences the site-directed cleavage of ribonuclease H using chimeric 2′-O-methyl oligodeoxyribonucleotides. Biochemistry. 29:1990;8793-8797.
55. Stein C.A., Krieg A.M. Problems in interpretation of data from in vitro and in vivo use of antisense oligodeoxynucleotides. Antisense Res. Dev. 4:1994;67-69.
56. Krieg A.M., Stein C.A. Phosphorothioate oligodeoxynucleotides: antisense or anti-protein? Antisense Res. Dev. 5:1995;241.
57. Crooke S.T. Proof of mechanism of antisense drugs. Antisense Nucleic Acids Drug Dev. 6:1996;145-147.
58. Matveeva O., Felden B., Audlin S., Gesteland R.F., Atkins J.F. 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. 25:1997;5010-5016.
59. Breaker R.R., Joyce G.F. A DNA enzyme that cleaves RNA. Chem. Biol. 1:1994;223-229.
60. Santoro S.W., Joyce G.F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA. 94:1997;4262-4266.
61. Pierce M.L., Ruffner D.E. Construction of a directed hammerhead ribozyme library: towards the identification of optimal target sites for antisense-mediated gene inhibition. Nucleic Acids Res. 26:1998;5093-5101.
62. Gewirtz A.M. Oligonucleotide therapeutics for human leukaemia. Chadwick D.J., Cardew G. Oligonucleotides as Therapeutic Agents. Ciba Foundation Symposium 209. 1997;169-194 Wiley, Chichester.
63. Struhl K. Ribonucleases. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K. Short Protocols in Molecular Biology. 1992;3.35-3.37 Wiley, New York.
64. Donis-Keller H., Maxam A.M., Gilbert W. Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 4:1977;2527-2538.