Strategy for designing specific antisense oligonucleotide sequences

Journal of Gastroenterology

Volumn 32, Issue 2, 1997, Pages 282-287

  Mitsuhashi, Masato ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Hitachi Chemical Research Center   (United States)

Author keywords

Antisense; Hybridization simulation; Oligonucleotides; Phosphorothioate; Software

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE;

GENE FUNCTION; HYBRIDIZATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SHORT SURVEY;

EID: 0030994906     PISSN: 09441174     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02936384     Document Type: Short Survey

References (37)

1. Zon G. Brief overview of control of genetic expression by antisense oligonucleotides and in vivo applications. Prospects for neurobiology. Mol Neurobiol 1995;10:219-229.
2. Crooke ST. Progress in antisense therapeutics. Hematol Pathol 1995;9:59-72.
3. Brysch W, Schlingensiepen KH. Design and application of antisense oligonucleotides in cell culture, in vivo, and as therapeutic agents. Cell Mol Neurobiol 1994;14:557-568.
4. Narayanan R. Antisense therapy of cancer. In Vivo 1994;8:787-793.
5. Agrawal S, Temsamani J, Galbraith W, et al. Pharmacokinetics of antisense oligonucleotides. Clin Pharmacokinet 1995;28:7-16.
6. Stein CA, Cheng Y-C. Antisense oligonucleotides as therapeutic agents. Is the bullet really magical? Science 1993;261;1004-1012.
7. Zhang R, Yan J, Shahinian H, et al. Pharmacokinetics of an anti-human immunodeficiency virus antisense oligodeoxynucleotide phosphorothioate (GEM 91) in HIV-infected subjects. Clin Pharmacol Ther 1995;58:44-53.
8. Wagner RW, Gene inhibition using antisense oligodeoxynucleotides. Nature 1994;372:333-335.
9. Egholm M, Buchardt O, Nielsen P, et al. Peptide nucleic acids (PNA). Oligonucleotide analogues with an achiral peptide backbone. J Am Chem Soc 1992;114:1895-1897.
10. Stirchak E, Summerton J, Weller D. Uncharged stereoregular nucleic acid analogs: 2. Morpholino nucleoside oligomers with carbamate internucleoside linkages. Nucleic Acids Res 1989;17: 6129-6141.
11. Stein C, Cohen J. Phosphorothioate oligonucleotide analog. In: Cohen J (ed) Oligonucleotides: Antisense inhibitors of gene expression. Boca Raton: CRC, 1989:97-117.
12. Mitsuhashi M, Cooper A, Ogura M, et al. Oligonucleotide probe design - a new approach. Nature 1994;367:759-761.
13. Hyndman D, Cooper A, Pruzinsky S, et al. Software to determine optimal oligonucleotide sequences based on thermodynamic hybridizability. Biotechniques 1996;20:1090-1097.
14. Breslauer KJ, Frank R, Blocker H, et al. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 1986;83:3746-3750.
15. Santa Lucia J, Allawi HT, Seneviratne PA. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 1996;35:3555-3562.
16. SantaLucia J, Kierzek R, Turner DH. Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 1990;29:8813-8819.
17. Sugimoto N, Kierzek R, Freier SM, et al. Energetics of internal GC mismatches in ribooligonucleotide helix. Biochemistry 1986; 25:5755-5759.
18. Fakler B, Herlitzer S, Amthor B, et al. Short antisense oligonucleotide-mediated inhibition is strongly dependent on oligo length and concentration but almost independent of location of the target sequence. J Biol Chem 1994;269:16187-16194.
19. Spearman M, Taylor WR, Greenberg AH, et al. Antisense oligodeoxyribonucleotide inhibition of TGF-beta 1 gene expression and alterations in the growth and malignant properties of mouse fibrosarcoma cells. Gene 1994;149:25-29.
20. Moria BP, Johnston JF, Ecker DJ, et al. Selective inhibition of mutant Ha-ras mRNA expression by antisense oligonucleotides. J Biol Chem 1992;267:19954-19962.
21. Bennett CF, Condon TP, Grimm S, et al. Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides. J Immunol 1994;152:3530-3540.
22. Hodges D, Crooke ST. Inhibition of splicing of wild-type and mutated luciferase-adenovirus pre-mRNAs by antisense oligonucleotides. Mol Pharmacol 1995;48:905-918.
23. Giles RV, Spiller DG, Green JA, et al. Optimization of antisense oligodeoxynucleotide structure for targeting bcr-abl mRNA. Blood 1995;86:744-754.
24. Pari GS, Field AK, Smith JA. Potent antiviral activity of an antisense oligonucleotide complementary to the intron-exon boundary of human cytomegalovirus genes UL36 and UL37. Antimicrob Agents Chemother 1995;39:1157-1161.
25. Wilbur WJ, Lipman DJ. Rapid similarity searches of nucleic acid and protein data banks. Proc Natl Acad Sci USA 1983;80:726-730.
26. Pearson WR, Lipman DJ. Improved tools for biological sequence analysis. Proc Natl Acad Sci USA 1988;85:2444-2448.
27. Smith TF, Waterman MS. Comparison of bio-sequences. Adv Appl Math 1981;2:482-489.
28. Turner DH, Sugimoto N, Freier SM. RNA structure prediction. Ann Rev Biophys Chem 1988;17:167-192.
29. Sugimoto N, Nakano S, Katho M, et al. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 1995;34:11211-11216.
30. Mitsuhashi M. Method of determining optimal PCR primers. Protein Nucleic Acid Enzyme 1996;41:439-445.
31. Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci USA 1989;86: 7706-7710.
32. Marschall P, Thomson JB, Eckstein F. Inhibition of gene expression with ribozymes. Cell Mol Neurobiol 1994;14:523-538.
33. Dean NM, McKay R. Inhibition of protein kinase C-alpha expression in mice after systemic administration of phosphorothioate antisense oligodeoxynucleotides. Proc Natl Acad Sci USA 1994; 91:11762-11766.
34. Wollnik F, Brysch W, Uhlmann E, et al. Block of c-Fos and JunB expression by antisense oligonucleotides inhibits light-induced phase shifts of the mammalian circadian clock. Eur J Neurosci 1995;7:388-393.
35. Burch RM, Mahan LC. Oligonucleotides antisense to the interleukin 1 receptor mRNA block the effects of interleukin 1 in cultured murine and human fibroblasts and in mice. J Clin Invest 1991;88:1190-1196.
36. Ensoli B, Markham P, Kao V, et al. Block of AIDS-Kaposi's sarcoma (KS) cell growth, angiogenesis, and lesion formation in nude mice by antisense oligonucleotide targeting basic fibroblast growth factor. A novel strategy for the therapy of KS. J Clin Invest 1994;94:1736-1746.
37. Raffa RB, Martinez RP, Connelly CD. G-protein antisense oligodeoxyribonucleotides and mu-opioid supraspinal antinociception. Eur J Pharmacol 1994;258:R5-7.