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Published on: January 20, 2016
PAM-adjacent DNA flexibility tunes CRISPR-Cas12a off-target binding
Aleique Allen1, Brendon H Cooper2,3, Jaideep Singh1
1Department of Chemistry, University of Southern California, 3430 S Vermont Ave., Los Angeles, CA, 90089, USA.
DNA flexibility near the protospacer-adjacent motif (PAM) influences Cas12a nuclease off-target binding. Unpairing at PAM+1, +2, and +3 positions increases Cas12a off-target activity, impacting genome editing applications.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Cas12a is a CRISPR-associated nuclease used for genome manipulation.
- DNA flexibility adjacent to the protospacer-adjacent motif (PAM) is implicated in Cas12a target recognition.
Purpose of the Study:
- To investigate the relationship between PAM-adjacent DNA flexibility and Cas12a off-target binding.
- To understand how DNA sequence variations near the PAM affect Cas12a specificity.
Main Methods:
- Adapted a SELEX-seq approach to analyze DNA-DNA mismatches at PAM+1 to +6 positions.
- In vitro binding assays with FnCas12a were performed using a DNA library with mismatches.
- Sequencing of bound and unbound DNA populations determined off-target binding propensity.
Main Results:
- Cas12a off-target binding is dependent on PAM-adjacent DNA flexibility.
- Unpairing of the protospacer at PAM+1 is required for off-target binding.
- Off-target binding increases with unpairing at PAM+2 and +3 positions.
Conclusions:
- PAM-adjacent DNA flexibility can modulate Cas12a off-target binding.
- Physical properties of DNA influence Cas12a target discrimination.
- Findings have implications for optimizing Cas12a-based genome editing tools.
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