Literature DB >> 15215363

TROD: T7 RNAi Oligo Designer.

Peter Dudek1, Didier Picard.   

Abstract

We have developed T7 RNAi Oligo Designer (TROD), a web application for RNA interference studies. TROD greatly facilitates the design of oligodeoxynucleotide sequences for the in vitro production of siRNA duplexes with T7 RNA polymerase. Given a query cDNA sequence, the program scans for appropriate target sequences based on the constraints of the T7 RNA polymerase method and published criteria for RNA interference with siRNAs. The output is an ordered and prioritized list of ready-to-order DNA oligonucleotide sequences, with links to perform a BLAST search to ascertain target sequence specificity. The TROD web service is available at http://www.cellbio.unige.ch/RNAi.html.

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Year:  2004        PMID： 15215363      PMCID： PMC441498          DOI： 10.1093/nar/gkh360

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  10 in total

1.  RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals.

Authors:  P D Zamore; T Tuschl; P A Sharp; D P Bartel
Journal:  Cell       Date:  2000-03-31       Impact factor: 41.582

2.  Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells.

Authors:  Patrick J Paddison; Amy A Caudy; Emily Bernstein; Gregory J Hannon; Douglas S Conklin
Journal:  Genes Dev       Date:  2002-04-15       Impact factor: 11.361

3.  RNA interference in mammalian cells using siRNAs synthesized with T7 RNA polymerase.

Authors:  Olivier Donzé; Didier Picard
Journal:  Nucleic Acids Res       Date:  2002-05-15       Impact factor: 16.971

4.  Asymmetry in the assembly of the RNAi enzyme complex.

Authors:  Dianne S Schwarz; György Hutvágner; Tingting Du; Zuoshang Xu; Neil Aronin; Phillip D Zamore
Journal:  Cell       Date:  2003-10-17       Impact factor: 41.582

5.  Functional siRNAs and miRNAs exhibit strand bias.

Authors:  Anastasia Khvorova; Angela Reynolds; Sumedha D Jayasena
Journal:  Cell       Date:  2003-10-17       Impact factor: 41.582

6.  High-throughput selection of effective RNAi probes for gene silencing.

Authors:  Rajeev Kumar; Douglas S Conklin; Vivek Mittal
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

Review 7.  Killing the messenger: short RNAs that silence gene expression.

Authors:  Derek M Dykxhoorn; Carl D Novina; Phillip A Sharp
Journal:  Nat Rev Mol Cell Biol       Date:  2003-06       Impact factor: 94.444

8.  The Bioperl toolkit: Perl modules for the life sciences.

Authors:  Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal:  Genome Res       Date:  2002-10       Impact factor: 9.043

9.  Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.

Authors:  J F Milligan; D R Groebe; G W Witherell; O C Uhlenbeck
Journal:  Nucleic Acids Res       Date:  1987-11-11       Impact factor: 16.971

10.  Analysis of gene function in somatic mammalian cells using small interfering RNAs.

Authors:  Sayda M Elbashir; Jens Harborth; Klaus Weber; Thomas Tuschl
Journal:  Methods       Date:  2002-02       Impact factor: 3.608
  10 in total
  6 in total

Review 1.  Silence of the transcripts: RNA interference in medicine.

Authors:  Sailen Barik
Journal:  J Mol Med (Berl)       Date:  2005-07-19       Impact factor: 4.599

2.  Direct comparison of the specificity of gene silencing using antisense oligonucleotides and RNAi.

Authors:  Benoit Bilanges; David Stokoe
Journal:  Biochem J       Date:  2005-06-01       Impact factor: 3.857

3.  Essential notes regarding the design of functional siRNAs for efficient mammalian RNAi.

Authors:  Kumiko Ui-Tei; Yuki Naito; Kaoru Saigo
Journal:  J Biomed Biotechnol       Date:  2006

4.  AMOD: a morpholino oligonucleotide selection tool.

Authors:  Eric W Klee; Kyong Jin Shim; Michael A Pickart; Stephen C Ekker; Lynda B M Ellis
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

5.  Effect of small interfering RNAs on matrix metalloproteinase 1 expression.

Authors:  Gen-Hung Chen; Chun-Hua Huang; Huang-Yao Luo; Shann-Tzong Jiang
Journal:  Biotechnol Rep (Amst)       Date:  2014-07-20

6.  Characterization of the essential role of bone morphogenetic protein 9 (BMP9) in osteogenic differentiation of mesenchymal stem cells (MSCs) through RNA interference.

Authors:  Shujuan Yan; Ruyi Zhang; Ke Wu; Jing Cui; Shifeng Huang; Xiaojuan Ji; Liping An; Chengfu Yuan; Cheng Gong; Linghuan Zhang; Wei Liu; Yixiao Feng; Bo Zhang; Zhengyu Dai; Yi Shen; Xi Wang; Wenping Luo; Bo Liu; Rex C Haydon; Michael J Lee; Russell R Reid; Jennifer Moriatis Wolf; Qiong Shi; Hue H Luu; Tong-Chuan He; Yaguang Weng
Journal:  Genes Dis       Date:  2018-04-27
  6 in total

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