In vitro Cleavage and Electrophoretic Mobility Shift Assays for Very Fast CRISPR

Roger S Zou; Yang Liu; Taekjip Ha

doi:10.21769/BioProtoc.4138

In vitro Cleavage and Electrophoretic Mobility Shift Assays for Very Fast CRISPR

Bio Protoc. 2021 Sep 5;11(17):e4138. doi: 10.21769/BioProtoc.4138.

Authors

Roger S Zou¹, Yang Liu², Taekjip Ha^{1

2

3

4}

Affiliations

¹ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
² Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, Maryland, USA.
³ Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA.
⁴ Howard Hughes Medical Institute, Baltimore, Maryland, USA.

Abstract

CRISPR-Cas9 has transformed biomedical research and medicine through convenient and targeted manipulation of DNA. Time- and spatially-resolved control over Cas9 activity through the recently developed very fast CRISPR (vfCRISPR) system have facilitated comprehensive studies of DNA damage and repair. Understanding the fundamental principles of Cas9 binding and cleavage behavior is essential before the widespread use of these systems and can be readily accomplished in vitro through both cleavage and electrophoretic mobility shift assays (EMSA). The protocol for in vitro cleavage consists of Cas9 with guide RNA (gRNA) ribonucleoprotein (RNP) formation, followed by incubation with target DNA. For EMSA, this reaction is directly loaded onto an agarose gel for visualization of the target DNA band that is shifted due to binding by the Cas9 RNP. To assay for cleavage, Proteinase K is added to degrade the RNP, allowing target DNA (cleaved and/or uncleaved) to migrate consistently with its molecular weight. Heating at 95°C rapidly inactivates the RNP on demand, allowing time-resolved measurements of Cas9 cleavage kinetics. This protocol facilitates the characterization of the light-activation mechanism of photocaged vfCRISPR gRNA.

Keywords: CRISPR-Cas9; Cleavage; EMSA; Electrophoretic mobility shift assay; Genome editing; In vitro.

Abstract

Grants and funding