메뉴 건너뛰기




Volumn 105, Issue 2, 2015, Pages 123-130

A computational analysis of antisense off-targets in prokaryotic organisms

Author keywords

Antisense gene silencing; Bacteria; Disinfection

Indexed keywords

ACPP GENE; ANTISENSE GENE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; ESCHERICHIA COLI K 12; GENE LOCATION; GENE SILENCING; GENE TARGETING; GENETIC ALGORITHM; HYBRID; INO1 GENE; MARORAB GENE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROKARYOTE; TRANSCRIPTOMICS; ALGORITHM; BIOLOGY; CHEMISTRY; METABOLISM; PROCEDURES; SEQUENCE ALIGNMENT;

EID: 84922730280     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2014.11.010     Document Type: Article
Times cited : (1)

References (42)
  • 1
  • 2
    • 26444491047 scopus 로고    scopus 로고
    • Resistance to antibiotics: Are we in the post-antibiotic era?
    • Alanis A.J. Resistance to antibiotics: Are we in the post-antibiotic era?. Arch. Med. Res. 2005, 36:697-705.
    • (2005) Arch. Med. Res. , vol.36 , pp. 697-705
    • Alanis, A.J.1
  • 4
    • 33750986817 scopus 로고    scopus 로고
    • Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation
    • Shao Y., Wu Y., Chan C.Y., McDonough K., Ding Y. Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation. Nucleic Acids Res. 2006, 34:5660-5669.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 5660-5669
    • Shao, Y.1    Wu, Y.2    Chan, C.Y.3    McDonough, K.4    Ding, Y.5
  • 5
    • 84856431819 scopus 로고    scopus 로고
    • RNA therapeutics: beyond RNA interference and antisense oligonucleotides
    • Kole R., Krainer A.R., Altman S. RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat. Rev. Drug Discov. 2012, 11:125-140.
    • (2012) Nat. Rev. Drug Discov. , vol.11 , pp. 125-140
    • Kole, R.1    Krainer, A.R.2    Altman, S.3
  • 6
    • 77951819895 scopus 로고    scopus 로고
    • Microbial inactivation of Pseudomonas putida and Pichia pastoris using gene silencing
    • Morse T.O., Morey S.J., Gunsch C.K. Microbial inactivation of Pseudomonas putida and Pichia pastoris using gene silencing. Environ. Sci. Technol. 2010, 44:3293-3297.
    • (2010) Environ. Sci. Technol. , vol.44 , pp. 3293-3297
    • Morse, T.O.1    Morey, S.J.2    Gunsch, C.K.3
  • 10
    • 0141924827 scopus 로고    scopus 로고
    • Inhibition of aminoglycoside 6'-N-acetyltransferase type Ib-mediated amikacin resistance by antisense oligodeoxynucleotides
    • Sarno R., Ha H., Weinsetel N., Tolmasky M.E. Inhibition of aminoglycoside 6'-N-acetyltransferase type Ib-mediated amikacin resistance by antisense oligodeoxynucleotides. Antimicrob. Agents Chemother. 2003, 47:3296-3304.
    • (2003) Antimicrob. Agents Chemother. , vol.47 , pp. 3296-3304
    • Sarno, R.1    Ha, H.2    Weinsetel, N.3    Tolmasky, M.E.4
  • 11
    • 0034602726 scopus 로고    scopus 로고
    • Treatment of Mycobacterium tuberculosis with antisense oligonucleotides to glutamine synthetase mRNA inhibits glutamine synthetase activity, formation of the poly-L-glutamate/glutamine cell wall structure, and bacterial replication
    • Harth G., Zamecnik P.C., Tang J.Y., Tabatadze D., Horwitz M.A. Treatment of Mycobacterium tuberculosis with antisense oligonucleotides to glutamine synthetase mRNA inhibits glutamine synthetase activity, formation of the poly-L-glutamate/glutamine cell wall structure, and bacterial replication. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:418-423.
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 418-423
    • Harth, G.1    Zamecnik, P.C.2    Tang, J.Y.3    Tabatadze, D.4    Horwitz, M.A.5
  • 12
    • 33847356371 scopus 로고    scopus 로고
    • Inositol-1-phosphate synthetase mRNA as a new target for antisense inhibition of Mycobacterium tuberculosis
    • Li Y., Chen Z., Li X., Zhang H., Huang Q., Zhang Y., Xu S. Inositol-1-phosphate synthetase mRNA as a new target for antisense inhibition of Mycobacterium tuberculosis. J. Biotechnol. 2007, 128:726-734.
    • (2007) J. Biotechnol. , vol.128 , pp. 726-734
    • Li, Y.1    Chen, Z.2    Li, X.3    Zhang, H.4    Huang, Q.5    Zhang, Y.6    Xu, S.7
  • 13
    • 44649200454 scopus 로고    scopus 로고
    • Antisense, RNAi, and gene silencing strategies for therapy: Mission possible or impossible?
    • Rayburn E.R., Zhang R. Antisense, RNAi, and gene silencing strategies for therapy: Mission possible or impossible?. Drug Discov. Today 2008, 13:513-521.
    • (2008) Drug Discov. Today , vol.13 , pp. 513-521
    • Rayburn, E.R.1    Zhang, R.2
  • 15
    • 1542333740 scopus 로고    scopus 로고
    • The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli
    • Dryselius R., Aswasti S.K., Rajarao G.K., Nielsen P.E., Good L. The translation start codon region is sensitive to antisense PNA inhibition in Escherichia coli. Oligonucleotides 2003, 13:427-433.
    • (2003) Oligonucleotides , vol.13 , pp. 427-433
    • Dryselius, R.1    Aswasti, S.K.2    Rajarao, G.K.3    Nielsen, P.E.4    Good, L.5
  • 17
    • 84895868996 scopus 로고    scopus 로고
    • Species-selective killing of bacteria by antimicrobial peptide-PNAs
    • Mondhe M., Chessher A., Goh S., Good L., Stach J.E.M. Species-selective killing of bacteria by antimicrobial peptide-PNAs. PLoS ONE 2014, 9.
    • (2014) PLoS ONE , vol.9
    • Mondhe, M.1    Chessher, A.2    Goh, S.3    Good, L.4    Stach, J.E.M.5
  • 18
    • 0037072576 scopus 로고    scopus 로고
    • Prospects for cationic polymers in gene and oligonucleotide therapy against cancer
    • Merdan T., Kopecek J., Kissel T. Prospects for cationic polymers in gene and oligonucleotide therapy against cancer. Adv. Drug Deliv. Rev. 2002, 54:715-758.
    • (2002) Adv. Drug Deliv. Rev. , vol.54 , pp. 715-758
    • Merdan, T.1    Kopecek, J.2    Kissel, T.3
  • 20
    • 17844387370 scopus 로고    scopus 로고
    • A computational study of off-target effects of RNA interference
    • Qiu S., Adema C.M., Lane T. A computational study of off-target effects of RNA interference. Nucleic Acids Res. 2005, 33:1834-1847.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1834-1847
    • Qiu, S.1    Adema, C.M.2    Lane, T.3
  • 22
    • 3242891277 scopus 로고    scopus 로고
    • DEQOR: a web-based tool for the design and quality control of siRNAs
    • Henschel A., Buchholz F., Habermann B. DEQOR: a web-based tool for the design and quality control of siRNAs. Nucleic Acids Res. 2004, 32:W113-W120.
    • (2004) Nucleic Acids Res. , vol.32 , pp. W113-W120
    • Henschel, A.1    Buchholz, F.2    Habermann, B.3
  • 23
    • 23144436831 scopus 로고    scopus 로고
    • DsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference
    • Naito Y., Yamada T., Matsumiya T., Ui-Tei K., Saigo K., Morishita S. dsCheck: highly sensitive off-target search software for double-stranded RNA-mediated RNA interference. Nucleic Acids Res. 2005, 33:W589-W591.
    • (2005) Nucleic Acids Res. , vol.33 , pp. W589-W591
    • Naito, Y.1    Yamada, T.2    Matsumiya, T.3    Ui-Tei, K.4    Saigo, K.5    Morishita, S.6
  • 24
    • 17444383131 scopus 로고    scopus 로고
    • Accelerated off-target search algorithm for siRNA
    • Yamada T., Morishita S. Accelerated off-target search algorithm for siRNA. Bioinformatics 2005, 21:1316-1324.
    • (2005) Bioinformatics , vol.21 , pp. 1316-1324
    • Yamada, T.1    Morishita, S.2
  • 27
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding Y., Chan C.Y., Lawrence C.E. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res. 2004, 32:W135-W141.
    • (2004) Nucleic Acids Res. , vol.32 , pp. W135-W141
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 30
    • 0030057861 scopus 로고    scopus 로고
    • Effects of oligonucleotide length, mismatches and mRNA levels on C-5 propyne-modified antisense potency
    • Flanagan W.M., Kothavale A., Wagner R.W. Effects of oligonucleotide length, mismatches and mRNA levels on C-5 propyne-modified antisense potency. Nucleic Acids Res. 1996, 24:2936-2941.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 2936-2941
    • Flanagan, W.M.1    Kothavale, A.2    Wagner, R.W.3
  • 32
    • 0034520771 scopus 로고    scopus 로고
    • Assessment of compositional heterogeneity within and between eukaryotic genomes
    • Nekrutenko A., Li W.H. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 2000, 10:1986-1995.
    • (2000) Genome Res. , vol.10 , pp. 1986-1995
    • Nekrutenko, A.1    Li, W.H.2
  • 33
    • 0027399409 scopus 로고
    • In vitro evaluation of phosphorothioate oligonucleotides targeted to the E2 messenger RNA of papillomavirus - potential treatment for genital warts
    • Cowsert L.M., Fox M.C., Zon G., Mirabelli C.K. In vitro evaluation of phosphorothioate oligonucleotides targeted to the E2 messenger RNA of papillomavirus - potential treatment for genital warts. Antimicrob. Agents Chemother. 1993, 37:171-177.
    • (1993) Antimicrob. Agents Chemother. , vol.37 , pp. 171-177
    • Cowsert, L.M.1    Fox, M.C.2    Zon, G.3    Mirabelli, C.K.4
  • 34
    • 33750061917 scopus 로고    scopus 로고
    • Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants
    • Xu P., Zhang Y., Kang L., Roossinck M.J., Mysore K.S. Computational estimation and experimental verification of off-target silencing during posttranscriptional gene silencing in plants. Plant Physiol. 2006, 142:429-440.
    • (2006) Plant Physiol. , vol.142 , pp. 429-440
    • Xu, P.1    Zhang, Y.2    Kang, L.3    Roossinck, M.J.4    Mysore, K.S.5
  • 35
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 36
    • 84895868996 scopus 로고    scopus 로고
    • Species-selective killing of bacteria by antimicrobial peptide-PNAs
    • Mondhe M., Chessher A., Goh S., Good L., Stach J.E.M. Species-selective killing of bacteria by antimicrobial peptide-PNAs. PLoS One 2014, 9:e89082.
    • (2014) PLoS One , vol.9 , pp. e89082
    • Mondhe, M.1    Chessher, A.2    Goh, S.3    Good, L.4    Stach, J.E.M.5
  • 38
    • 79952589852 scopus 로고    scopus 로고
    • A k-mer scheme to predict piRNAs and characterize locust piRNAs
    • Zhang Y., Wang X., Kang L. A k-mer scheme to predict piRNAs and characterize locust piRNAs. Bioinformatics 2011, 27:771-776.
    • (2011) Bioinformatics , vol.27 , pp. 771-776
    • Zhang, Y.1    Wang, X.2    Kang, L.3
  • 39
    • 67649479403 scopus 로고    scopus 로고
    • Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli
    • Goh S., Boberek J.M., Nakashima N., Stach J., Good L. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS ONE 2009, 4.
    • (2009) PLoS ONE , vol.4
    • Goh, S.1    Boberek, J.M.2    Nakashima, N.3    Stach, J.4    Good, L.5
  • 41
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • Zhang R., Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res. 2009, 37:D455-D458.
    • (2009) Nucleic Acids Res. , vol.37 , pp. D455-D458
    • Zhang, R.1    Lin, Y.2
  • 42
    • 0032696759 scopus 로고    scopus 로고
    • Addiction modules and programmed cell death and antideath in bacterial cultures
    • Engelberg-Kulka H., Glaser G. Addiction modules and programmed cell death and antideath in bacterial cultures. Annu. Rev. Microbiol. 1999, 53:43-70.
    • (1999) Annu. Rev. Microbiol. , vol.53 , pp. 43-70
    • Engelberg-Kulka, H.1    Glaser, G.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.