Comprehensive analysis of the specificity of transcription activator-like effector nucleases
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Comprehensive analysis of the specificity of transcription activator-like effector nucleases. / Juillerat, Alexandre; Dubois, Gwendoline; Valton, Julien; Thomas, Séverine; Stella, Stefano; Maréchal, Alan; Langevin, Stéphanie; Benomari, Nassima; Bertonati, Claudia; Silva, George H; Daboussi, Fayza; Epinat, Jean-Charles; Montoya, Guillermo; Duclert, Aymeric; Duchateau, Philippe.
In: Nucleic Acids Research, Vol. 42, No. 8, 04.2014, p. 5390-402.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Comprehensive analysis of the specificity of transcription activator-like effector nucleases
AU - Juillerat, Alexandre
AU - Dubois, Gwendoline
AU - Valton, Julien
AU - Thomas, Séverine
AU - Stella, Stefano
AU - Maréchal, Alan
AU - Langevin, Stéphanie
AU - Benomari, Nassima
AU - Bertonati, Claudia
AU - Silva, George H
AU - Daboussi, Fayza
AU - Epinat, Jean-Charles
AU - Montoya, Guillermo
AU - Duclert, Aymeric
AU - Duchateau, Philippe
PY - 2014/4
Y1 - 2014/4
N2 - A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only accommodate a relatively small number of position-dependent mismatches while maintaining a detectable activity at endogenous loci in vivo, demonstrating the high specificity of these molecular tools. We thus envision that the results we provide will allow for more deliberate choices of DNA binding arrays and/or DNA targets, extending our engineering capabilities.
AB - A key issue when designing and using DNA-targeting nucleases is specificity. Ideally, an optimal DNA-targeting tool has only one recognition site within a genomic sequence. In practice, however, almost all designer nucleases available today can accommodate one to several mutations within their target site. The ability to predict the specificity of targeting is thus highly desirable. Here, we describe the first comprehensive experimental study focused on the specificity of the four commonly used repeat variable diresidues (RVDs; NI:A, HD:C, NN:G and NG:T) incorporated in transcription activator-like effector nucleases (TALEN). The analysis of >15 500 unique TALEN/DNA cleavage profiles allowed us to monitor the specificity gradient of the RVDs along a TALEN/DNA binding array and to present a specificity scoring matrix for RVD/nucleotide association. Furthermore, we report that TALEN can only accommodate a relatively small number of position-dependent mismatches while maintaining a detectable activity at endogenous loci in vivo, demonstrating the high specificity of these molecular tools. We thus envision that the results we provide will allow for more deliberate choices of DNA binding arrays and/or DNA targets, extending our engineering capabilities.
KW - Amino Acids
KW - Animals
KW - Base Sequence
KW - CHO Cells
KW - Cricetinae
KW - Cricetulus
KW - DNA
KW - DNA Cleavage
KW - DNA-Binding Proteins
KW - Deoxyribonucleases
KW - Mutation
KW - Protein Array Analysis
KW - Protein Engineering
KW - Yeasts
U2 - 10.1093/nar/gku155
DO - 10.1093/nar/gku155
M3 - Journal article
C2 - 24569350
VL - 42
SP - 5390
EP - 5402
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 8
ER -
ID: 138735073