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Mouse Genome Engineering Using Designer Nucleases
Published on: April 2, 2014
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SAPTA: a new design tool for improving TALE nuclease activity
Yanni Lin1, Eli J Fine, Zhilan Zheng
1Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA and Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
Nucleic Acids Research
|January 21, 2014
Summary
A new online tool, SAPTA (Scoring Algorithm for Predicting TALEN Activity), improves genome editing by optimizing Transcription activator-like effector nuclease (TALEN) designs. SAPTA enhances TALEN activity and gene modification efficiency for researchers.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genetics
Background:
- Transcription activator-like effector nucleases (TALENs) are powerful genome editing tools.
- Existing TALEN design guidelines require user-friendly tools for optimal design and robust editing.
Purpose of the Study:
- To evaluate existing TALEN design guidelines.
- To develop new, optimized TALEN design guidelines.
- To establish SAPTA, an online tool for predicting TALEN activity and selecting optimal TALEN pairs.
Main Methods:
- Evaluation of 205 TALENs to establish new design guidelines.
- Development of the Scoring Algorithm for Predicting TALEN Activity (SAPTA).
- Implementation of SAPTA as an online design tool for ranking potential TALEN target sites.
Main Results:
- SAPTA-based TALEN designs increased average intracellular TALEN monomer activity by over 3-fold.
- Achieved an average endogenous gene-modification frequency of 39%.
- Demonstrated improved efficiency, particularly for TALENs with the NK di-residue.
Conclusions:
- SAPTA is a useful and flexible tool for designing highly active TALENs.
- The tool facilitates selection of optimal TALEN pairs for genome editing applications.
- SAPTA is accessible online at http://baolab.bme.gatech.edu/Research/BioinformaticTools/TAL_targeter.html.
