Quantification of CRISPR-Cas9 diffusion dynamics in Escherichia coli
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Date
04/08/2020Item status
Restricted AccessEmbargo end date
04/08/2021Author
Zaoui, Xavier Karim
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Abstract
What do adaptive immunity, genetic engineering and antimicrobials have in common?
CRISPR-Cas9, the popular enzymatic complex that produces DNA double-strand breaks when
associated with a guide-RNA. Hundreds of labs routinely use this system to edit genomic DNA;
however, some of the mechanisms by which it interacts with nucleic acid remain unclear.
In my lab, we developed an expertise in the study of DNA recombination, DNA repair and
DNA interactions in Escherichia coli. We use single-molecule fluorescent microscopy to
collect images in real time, in vivo. During my PhD, I harnessed this expertise to follow the
behaviour of the Cas9 protein under different conditions: various expression levels; various
gRNAs; and various genomic targets. By observing the diffusion dynamics of the protein, I
was able to quantify how different DNA interactions were impacting the motion of the protein
in the cytoplasm and inferred that actual ON-target interactions were very rare throughout the
lifetime of the protein. In contrast, the protein was mainly involved in non-specific OFF-target
DNA interactions, in search of its actual target. Additionally, my results reveal the presence of
a large fraction of non-specific interactions, hitherto not reported in the literature, owing to
their absence of DNA modification.
In total, this work offers a collection of highly quantitative measurements on the behaviour of
a protein whose activity is central to many biologists, while shedding a new light on the
importance of Cas9 searching and targeting mechanisms. Finally, it opens a discussion on the
role of DNA recognition in the context of gene editing and antimicrobial resistance.