SAPTA: a new design tool for improving TALE nuclease activity.
Transcription activator-like effector nucleases (TALENs) have become a powerful tool for genome editing due to the simple code linking the amino acid sequences of their DNA-binding domains to TALEN nucleotide targets. While the initial TALEN-design guidelines are very useful, user-friendly tools defining optimal TALEN designs for robust genome editing need to be developed. Here we evaluated existing guidelines and developed new design guidelines for TALENs based on 205 TALENs tested, and established the scoring algorithm for predicting TALEN activity (SAPTA) as a new online design tool. For any input gene of interest, SAPTA gives a ranked list of potential TALEN target sites, facilitating the selection of optimal TALEN pairs based on predicted activity. SAPTA-based TALEN designs increased the average intracellular TALEN monomer activity by >3-fold, and resulted in an average endogenous gene-modification frequency of 39% for TALENs containing the repeat variable di-residue NK that favors specificity rather than activity. It is expected that SAPTA will become a useful and flexible tool for designing highly active TALENs for genome-editing applications. SAPTA can be accessed via the website at http://baolab.bme.gatech.edu/Research/BioinformaticTools/TAL_targeter.html.
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA and Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
Yanni
Y
Lin
Eli J
EJ
Fine
Zhilan
Z
Zheng
Christopher J
CJ
Antico
Richard A
RA
Voit
Matthew H
MH
Porteus
Thomas J
TJ
Cradick
Gang
G
Bao
D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D003851:Deoxyribonucleases / Q000378:metabolism*; D057809:HEK293 Cells; D006801:Humans; D012984:Software
D004268:DNA-Binding Proteins; D004247:DNA; D003851:Deoxyribonucleases