메뉴 건너뛰기




Volumn 18, Issue 12, 2002, Pages 1567-1575

Computational antisense oligo prediction with a neural network model

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; MESSENGER RNA;

EID: 0036953263     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.12.1567     Document Type: Article
Times cited : (37)

References (43)
  • 2
    • 0034327531 scopus 로고    scopus 로고
    • Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes
    • Amarzguioui,M., Brede,G., Babaie,E., Grotli,M., Sproat,B. and Prydz,H. (2000) Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes. Nucleic Acids Res., 28, 4113-4124.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4113-4124
    • Amarzguioui, M.1    Brede, G.2    Babaie, E.3    Grotli, M.4    Sproat, B.5    Prydz, H.6
  • 3
    • 0026020219 scopus 로고
    • Walking along human c-myc mRNA with antisense oligodeoxynucleotides: Maximum efficacy at the 5′ cap region
    • Bacon,T.A. and Wickstrom,E. (1991) Walking along human c-myc mRNA with antisense oligodeoxynucleotides: maximum efficacy at the 5′ cap region. Oncogene Res., 6, 13-19.
    • (1991) Oncogene Res. , vol.6 , pp. 13-19
    • Bacon, T.A.1    Wickstrom, E.2
  • 5
    • 0028220670 scopus 로고
    • Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides
    • Bennett,C.F., Condon,T.P., Grimm,S., Chan,H. and Chiang,M.Y. (1994) Inhibition of endothelial cell adhesion molecule expression with antisense oligonucleotides. J. Immunol., 152, 3530-3540.
    • (1994) J. Immunol. , vol.152 , pp. 3530-3540
    • Bennett, C.F.1    Condon, T.P.2    Grimm, S.3    Chan, H.4    Chiang, M.Y.5
  • 6
    • 0026052924 scopus 로고
    • Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms
    • Chiang,M.Y., Chan,H., Zounes,M.A., Freier,S.M., Lima,W.F. and Bennett,C.F. (1991) Antisense oligonucleotides inhibit intercellular adhesion molecule 1 expression by two distinct mechanisms. J. Biol. Chem., 266, 18162-18171.
    • (1991) J. Biol. Chem. , vol.266 , pp. 18162-18171
    • Chiang, M.Y.1    Chan, H.2    Zounes, M.A.3    Freier, S.M.4    Lima, W.F.5    Bennett, C.F.6
  • 7
    • 0027459559 scopus 로고
    • Use of an antisense oligonucleotide to inhibit expression of a mutated human procollagen gene (COL1A1) in transfected mouse 3T3 cells
    • Colige,A., Sokolov,B.P., Nugent,P., Baserga,R. and Prockop,D.J. (1993) Use of an antisense oligonucleotide to inhibit expression of a mutated human procollagen gene (COL1A1) in transfected mouse 3T3 cells. Biochemistry, 32, 7-11.
    • (1993) Biochemistry , vol.32 , pp. 7-11
    • Colige, A.1    Sokolov, B.P.2    Nugent, P.3    Baserga, R.4    Prockop, D.J.5
  • 8
    • 0033990403 scopus 로고    scopus 로고
    • Progress in antisense technology: The end of the beginning
    • Crooke,S.T. (2000) Progress in antisense technology: the end of the beginning. Methods Enzymol., 313, 3-45.
    • (2000) Methods Enzymol. , vol.313 , pp. 3-45
    • Crooke, S.T.1
  • 9
    • 0028292570 scopus 로고
    • Inhibition of protein kinase C-alpha expression in human A549 cells by antisense oligonucleotides inhibits induction of intercellular adhesion molecule 1 (ICAM-1) mRNA by phorbol esters
    • Dean,N.M., McKay,R., Condon,T.P. and Bennett,C.F. (1994) Inhibition of protein kinase C-alpha expression in human A549 cells by antisense oligonucleotides inhibits induction of intercellular adhesion molecule 1 (ICAM-1) mRNA by phorbol esters. J. Biol. Chem., 269, 16416-16424.
    • (1994) J. Biol. Chem. , vol.269 , pp. 16416-16424
    • Dean, N.M.1    McKay, R.2    Condon, T.P.3    Bennett, C.F.4
  • 10
    • 0021760092 scopus 로고
    • A comprehensive set of sequence analysis programs for the VAX
    • Devereux,J., Haeberli,P. and Smithies,O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res., 12, 387-395.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 387-395
    • Devereux, J.1    Haeberli, P.2    Smithies, O.3
  • 11
    • 0035283171 scopus 로고    scopus 로고
    • Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
    • Ding,Y. and Lawrence,C.E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res., 29, 1034-1046.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1034-1046
    • Ding, Y.1    Lawrence, C.E.2
  • 12
    • 0028920561 scopus 로고
    • Mitogen-activated protein (MAP) kinase is regulated by the MAP kinase phosphatase (MKP-1) in vascular smooth muscle cells. Effect of actinomycin D and antisense oligonucleotides
    • Duff,J.L., Monia,B.P. and Berk,B.C. (1995) Mitogen-activated protein (MAP) kinase is regulated by the MAP kinase phosphatase (MKP-1) in vascular smooth muscle cells. Effect of actinomycin D and antisense oligonucleotides. J. Biol. Chem., 270, 7161-7166.
    • (1995) J. Biol. Chem. , vol.270 , pp. 7161-7166
    • Duff, J.L.1    Monia, B.P.2    Berk, B.C.3
  • 13
    • 0033665573 scopus 로고    scopus 로고
    • ODNBase-a web database for antisense oligonucleotide effectiveness studies
    • Giddings,M.C., Matveeva,O.V., Atkins,J.F. and Gesteland,R.F. (2000) ODNBase-a web database for antisense oligonucleotide effectiveness studies. Bioinformatics, 16, 843-844.
    • (2000) Bioinformatics , vol.16 , pp. 843-844
    • Giddings, M.C.1    Matveeva, O.V.2    Atkins, J.F.3    Gesteland, R.F.4
  • 15
    • 0029938209 scopus 로고    scopus 로고
    • Potent antisense oligonucleotides to the human multidrug resistance-1 mRNA are rationally selected by mapping RNA-accessible sites with oligonucleotide libraries
    • Ho,S.P., Britton,D.H., Stone,B.A., Behrens,D.L., Leffet,L.M., Hobbs,F.W., Miller,J.A. and Trainor,G.L. (1996) 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, 1901-1907.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1901-1907
    • Ho, S.P.1    Britton, D.H.2    Stone, B.A.3    Behrens, D.L.4    Leffet, L.M.5    Hobbs, F.W.6    Miller, J.A.7    Trainor, G.L.8
  • 17
    • 0028822483 scopus 로고
    • Inhibition of splicing of wild-type and mutated luciferase-adenovirus pre-mRNAs by antisense oligonucleotides
    • Hodges,D. and Crooke,S.T. (1995) Inhibition of splicing of wild-type and mutated luciferase-adenovirus pre-mRNAs by antisense oligonucleotides. Mol. Pharmacol., 48, 905-918.
    • (1995) Mol. Pharmacol. , vol.48 , pp. 905-918
    • Hodges, D.1    Crooke, S.T.2
  • 18
    • 0027956640 scopus 로고
    • 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
    • Laptev,A.V., Lu,Z., Colige,A. and Prockop,D.J. (1994) 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, 11033-11039.
    • (1994) Biochemistry , vol.33 , pp. 11033-11039
    • Laptev, A.V.1    Lu, Z.2    Colige, A.3    Prockop, D.J.4
  • 19
    • 0029334957 scopus 로고
    • Antisense gene suppression against human ICAM-1, ELAM-1, and VCAM-1 in cultured human umbilical vein endothelial cells
    • Lee,C.H., Chen,H.H., Hoke,G., Jong,J.S., White,L. and Kang,Y.H. (1995) Antisense gene suppression against human ICAM-1, ELAM-1, and VCAM-1 in cultured human umbilical vein endothelial cells. Shock, 4, 1-10.
    • (1995) Shock , vol.4 , pp. 1-10
    • Lee, C.H.1    Chen, H.H.2    Hoke, G.3    Jong, J.S.4    White, L.5    Kang, Y.H.6
  • 20
    • 17344375268 scopus 로고    scopus 로고
    • Inhibition of human TNF alpha and LT in cell-free extracts and in cell culture by antisense oligonucleotides
    • 1317
    • Lefebvre d'Hellencourt,C., Diaw,L., Cornillet,P. and Guenounou,M. (1996) Inhibition of human TNF alpha and LT in cell-free extracts and in cell culture by antisense oligonucleotides. Biochim. Biophys. Acta, 1317, 168-174.
    • (1996) Biochim. Biophys. Acta , pp. 168-174
    • Lefebvre d'Hellencourt, C.1    Diaw, L.2    Cornillet, P.3    Guenounou, M.4
  • 21
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 23
    • 0032994533 scopus 로고    scopus 로고
    • Antisense oligodeoxynucleotides targeting internal exon sequences efficiently regulate TNF-alpha expression
    • Mayne,M., Ni,W., McKenna,R. and Power,C. (1999) Antisense oligodeoxynucleotides targeting internal exon sequences efficiently regulate TNF-alpha expression. Antisense Nucleic Acid Drug Dev., 9, 135-144.
    • (1999) Antisense Nucleic Acid Drug Dev. , vol.9 , pp. 135-144
    • Mayne, M.1    Ni, W.2    McKenna, R.3    Power, C.4
  • 24
    • 0030902471 scopus 로고    scopus 로고
    • Selecting effective antisense reagents on combinatorial oligonucleotide arrays
    • Milner,N., Mir,K.U. and Southern,E.M. (1997) Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat. Biotechnol., 15, 537-541.
    • (1997) Nat. Biotechnol. , vol.15 , pp. 537-541
    • Milner, N.1    Mir, K.U.2    Southern, E.M.3
  • 25
    • 0030130581 scopus 로고    scopus 로고
    • Inhibition of interleukin-1 type I receptor expression in human cell-lines by an antisense phosphorothioate oligodeoxynucleotide
    • Miraglia,L., Geiger,T., Bennett,C.F. and Dean,N.M. (1996) Inhibition of interleukin-1 type I receptor expression in human cell-lines by an antisense phosphorothioate oligodeoxynucleotide. Int. J. Immunopharmacol., 18, 227-240.
    • (1996) Int. J. Immunopharmacol. , vol.18 , pp. 227-240
    • Miraglia, L.1    Geiger, T.2    Bennett, C.F.3    Dean, N.M.4
  • 26
    • 0029977448 scopus 로고    scopus 로고
    • Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase
    • Monia,B.P., Johnston,J.F., Geiger,T., Muller,M. and Fabbro,D. (1996) Antitumor activity of a phosphorothioate antisense oligodeoxynucleotide targeted against C-raf kinase. Nat. Med., 2, 668-675.
    • (1996) Nat. Med. , vol.2 , pp. 668-675
    • Monia, B.P.1    Johnston, J.F.2    Geiger, T.3    Muller, M.4    Fabbro, D.5
  • 27
    • 0033975328 scopus 로고    scopus 로고
    • Sensible use of antisense: How to use oligonucleotides as research tools
    • Myers,K.J. and Dean,N.M. (2000) Sensible use of antisense: How to use oligonucleotides as research tools. Trends Pharmacol. Sci., 21, 19-23.
    • (2000) Trends Pharmacol. Sci. , vol.21 , pp. 19-23
    • Myers, K.J.1    Dean, N.M.2
  • 28
    • 0033570886 scopus 로고    scopus 로고
    • A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability
    • Patzel,V., Steidl,U., Kronenwett,R., Haas,R. and Sczakiel,G. (1999) A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. Nucleic Acids Res., 27, 4328-4334.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4328-4334
    • Patzel, V.1    Steidl, U.2    Kronenwett, R.3    Haas, R.4    Sczakiel, G.5
  • 30
    • 0034234550 scopus 로고    scopus 로고
    • RNA accessibility prediction: A theoretical approach is consistent with experimental studies in cell extracts
    • Scherr,M., Rossi,J.J., Sczakiel,G. and Patzel,V. (2000) RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. Nucleic Acids Res., 28, 2455-2461.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2455-2461
    • Scherr, M.1    Rossi, J.J.2    Sczakiel, G.3    Patzel, V.4
  • 31
    • 0000849430 scopus 로고    scopus 로고
    • Theoretical and experimental approaches to design effective antisense oligonucleotides
    • Sczakiel,G. (2000) Theoretical and experimental approaches to design effective antisense oligonucleotides. Front. Biosci., 5, D194-201.
    • (2000) Front Biosci. , vol.5
    • Sczakiel, G.1
  • 32
    • 0027289572 scopus 로고
    • Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1
    • Sczakiel,G., Homann,M. and Rittner,K. (1993) Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1. Antisense Res. Dev., 3, 45-52.
    • (1993) Antisense Res. Dev. , vol.3 , pp. 45-52
    • Sczakiel, G.1    Homann, M.2    Rittner, K.3
  • 33
    • 0033977659 scopus 로고    scopus 로고
    • Application of secondary structure prediction in antisense drug design targeting protein kinase C-alpha mRNA and QSAR analysis
    • Song,H.F., Tang,Z.M., Yuan,S.J. and Zhu,B.Z. (2000) Application of secondary structure prediction in antisense drug design targeting protein kinase C-alpha mRNA and QSAR analysis. Acta Pharmacol. Sin., 21, 80-86.
    • (2000) Acta Pharmacol. Sin. , vol.21 , pp. 80-86
    • Song, H.F.1    Tang, Z.M.2    Yuan, S.J.3    Zhu, B.Z.4
  • 34
    • 0027987972 scopus 로고
    • Blocking of heart allograft rejection by intercellular adhesion molecule-1 antisense oligonucleotides alone or in combination with other immunosuppressive modalities
    • Stepkowski,S.M., Tu,Y., Condon,T.P. and Bennett,C.F. (1994) Blocking of heart allograft rejection by intercellular adhesion molecule-1 antisense oligonucleotides alone or in combination with other immunosuppressive modalities. J. Immunol., 153, 5336-5346.
    • (1994) J. Immunol. , vol.153 , pp. 5336-5346
    • Stepkowski, S.M.1    Tu, Y.2    Condon, T.P.3    Bennett, C.F.4
  • 35
    • 0030071190 scopus 로고    scopus 로고
    • Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides
    • Stewart,A.J., Canitrot,Y., Baracchini,E., Dean,N.M., Deeley,R.G. and Cole,S.P. (1996) Reduction of expression of the multidrug resistance protein (MRP) in human tumor cells by antisense phosphorothioate oligonucleotides. Biochem. Pharmacol., 51, 461-469.
    • (1996) Biochem. Pharmacol. , vol.51 , pp. 461-469
    • Stewart, A.J.1    Canitrot, Y.2    Baracchini, E.3    Dean, N.M.4    Deeley, R.G.5    Cole, S.P.6
  • 36
    • 0030939071 scopus 로고    scopus 로고
    • In vivo antisense oligodeoxynucleotide mapping reveals masked regulatory elements in an mRNA dormant in mouse oocytes
    • Stutz,A., Huarte,J., Gubler,P., Conne,B., Belin,D. and Vassalli,J.D. (1997) In vivo antisense oligodeoxynucleotide mapping reveals masked regulatory elements in an mRNA dormant in mouse oocytes. Mol. Cell Biol., 17, 1759-1767.
    • (1997) Mol. Cell Biol. , vol.17 , pp. 1759-1767
    • Stutz, A.1    Huarte, J.2    Gubler, P.3    Conne, B.4    Belin, D.5    Vassalli, J.D.6
  • 38
    • 0029859713 scopus 로고    scopus 로고
    • Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes
    • Sugimoto,N., Nakano,S., Yoneyama,M. and Honda,K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. Nucleic Acids Res., 24, 4501-4505.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4501-4505
    • Sugimoto, N.1    Nakano, S.2    Yoneyama, M.3    Honda, K.4
  • 39
    • 0034429847 scopus 로고    scopus 로고
    • Influence of mRNA self-structure on hybridization: Computational tools for antisense sequence selection
    • Toschi,N. (2000) Influence of mRNA self-structure on hybridization: computational tools for antisense sequence selection. Methods, 22, 261-269.
    • (2000) Methods , vol.22 , pp. 261-269
    • Toschi, N.1
  • 40
    • 0032566621 scopus 로고    scopus 로고
    • Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design
    • Tu,G.C., Cao,Q.N., Zhou,F. and Israel,Y. (1998) Tetranucleotide GGGA motif in primary RNA transcripts. Novel target site for antisense design. J. Biol. Chem., 273, 25125-25131.
    • (1998) J. Biol. Chem. , vol.273 , pp. 25125-25131
    • Tu, G.C.1    Cao, Q.N.2    Zhou, F.3    Israel, Y.4
  • 41
    • 0034653783 scopus 로고    scopus 로고
    • Effects of RNA secondary structure on cellular antisense activity
    • Vickers,T.A., Wyatt,J.R. and Freier,S.M. (2000) Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res., 28, 1340-1347.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1340-1347
    • Vickers, T.A.1    Wyatt, J.R.2    Freier, S.M.3
  • 42
  • 43
    • 0033527352 scopus 로고    scopus 로고
    • Prediction of antisense oligonucleotide binding affinity to a structured RNA target
    • Walton,S.P., Stephanopoulos,G.N., Yarmush,M.L. and Roth,C.M. (1999) Prediction of antisense oligonucleotide binding affinity to a structured RNA target. Biotechnol. Bioeng., 65, 1-9.
    • (1999) Biotechnol. Bioeng. , vol.65 , pp. 1-9
    • Walton, S.P.1    Stephanopoulos, G.N.2    Yarmush, M.L.3    Roth, C.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.