Mojo Hand, a TALEN design tool for genome editing applications

Kevin L. Neff, David P. Argue, Alvin C. Ma, Han B. Lee, Karl J Clark, Stephen C Ekker

Research output: Contribution to journalArticle

54 Citations (Scopus)

Abstract

Background: Recent studies of transcription activator-like (TAL) effector domains fused to nucleases (TALENs) demonstrate enormous potential for genome editing. Effective design of TALENs requires a combination of selecting appropriate genetic features, finding pairs of binding sites based on a consensus sequence, and, in some cases, identifying endogenous restriction sites for downstream molecular genetic applications.Results: We present the web-based program Mojo Hand for designing TAL and TALEN constructs for genome editing applications (http://www.talendesign.org). We describe the algorithm and its implementation. The features of Mojo Hand include (1) automatic download of genomic data from the National Center for Biotechnology Information, (2) analysis of any DNA sequence to reveal pairs of binding sites based on a user-defined template, (3) selection of restriction-enzyme recognition sites in the spacer between the TAL monomer binding sites including options for the selection of restriction enzyme suppliers, and (4) output files designed for subsequent TALEN construction using the Golden Gate assembly method.Conclusions: Mojo Hand enables the rapid identification of TAL binding sites for use in TALEN design. The assembly of TALEN constructs, is also simplified by using the TAL-site prediction program in conjunction with a spreadsheet management aid of reagent concentrations and TALEN formulation. Mojo Hand enables scientists to more rapidly deploy TALENs for genome editing applications.

Original languageEnglish (US)
Article number1
JournalBMC Bioinformatics
Volume14
Issue number1
DOIs
StatePublished - Jan 16 2013

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Transcription
Binding sites
Genome
Hand
Genes
Binding Sites
Enzymes
Restriction
DNA sequences
Spreadsheets
Biotechnology
Monomers
Spreadsheet
Design
Gene Editing
Transcription Activator-Like Effectors
Information Centers
Consensus Sequence
DNA Sequence
Web-based

Keywords

  • Genome editing
  • TAL effector
  • TALEN

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Mojo Hand, a TALEN design tool for genome editing applications. / Neff, Kevin L.; Argue, David P.; Ma, Alvin C.; Lee, Han B.; Clark, Karl J; Ekker, Stephen C.

In: BMC Bioinformatics, Vol. 14, No. 1, 1, 16.01.2013.

Research output: Contribution to journalArticle

Neff, Kevin L. ; Argue, David P. ; Ma, Alvin C. ; Lee, Han B. ; Clark, Karl J ; Ekker, Stephen C. / Mojo Hand, a TALEN design tool for genome editing applications. In: BMC Bioinformatics. 2013 ; Vol. 14, No. 1.
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