Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a Article Swipe
Aakash Saha
,
Pablo R. Arantes
,
Rohaine V. Hsu
,
Yogesh B. Narkhede
,
Martin Jínek
,
Giulia Palermo
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jcim.0c00929
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jcim.0c00929
CRISPR-Cas12a is a genome-editing system, recently also harnessed for nucleic acid detection, which is promising for the diagnosis of the SARS-CoV-2 coronavirus through the DETECTR technology. Here, a collective ensemble of multimicrosecond molecular dynamics characterizes the key dynamic determinants allowing nucleic acid processing in CRISPR-Cas12a. We show that DNA binding induces a switch in the conformational dynamics of Cas12a, which results in the activation of the peripheral REC2 and Nuc domains to enable cleavage of nucleic acids. The simulations reveal that large-amplitude motions of the Nuc domain could favor the conformational activation of the system toward DNA cleavages. In this process, the REC lobe plays a critical role. Accordingly, the joint dynamics of REC and Nuc shows the tendency to prime the conformational transition of the DNA target strand toward the catalytic site. Most notably, the highly coupled dynamics of the REC2 region and Nuc domain suggests that REC2 could act as a regulator of the Nuc function, similar to what was observed previously for the HNH domain in the CRISPR-associated nuclease Cas9. These mutual domain dynamics could be critical for the nonspecific binding of DNA and thereby for the underlying mechanistic functioning of the DETECTR technology. Considering that REC is a key determinant in the system's specificity, our findings provide a rational basis for future biophysical studies aimed at characterizing its function in CRISPR-Cas12a. Overall, our outcomes advance our mechanistic understanding of CRISPR-Cas12a and provide grounds for novel engineering efforts to improve genome editing and viral detection.
Related Topics
Concepts
CRISPR
Nuclease
Computational biology
Cas9
Genome editing
DNA
Nucleic acid
Biology
Function (biology)
Guide RNA
Genome
Molecular dynamics
Biophysics
Chemistry
Genetics
Gene
Computational chemistry
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.jcim.0c00929
- https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00929
- OA Status
- bronze
- Cited By
- 58
- References
- 60
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3094098207
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W3094098207Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1021/acs.jcim.0c00929Digital Object Identifier
- Title
-
Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12aWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-10-27Full publication date if available
- Authors
-
Aakash Saha, Pablo R. Arantes, Rohaine V. Hsu, Yogesh B. Narkhede, Martin Jínek, Giulia PalermoList of authors in order
- Landing page
-
https://doi.org/10.1021/acs.jcim.0c00929Publisher landing page
- PDF URL
-
https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00929Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
bronzeOpen access status per OpenAlex
- OA URL
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https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00929Direct OA link when available
- Concepts
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CRISPR, Nuclease, Computational biology, Cas9, Genome editing, DNA, Nucleic acid, Biology, Function (biology), Guide RNA, Genome, Molecular dynamics, Biophysics, Chemistry, Genetics, Gene, Computational chemistryTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
58Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 9, 2024: 9, 2023: 17, 2022: 13, 2021: 8Per-year citation counts (last 5 years)
- References (count)
-
60Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| countries_distinct_count | 2 |
| institutions_distinct_count | 6 |
| corresponding_institution_ids | https://openalex.org/I103635307 |
| citation_normalized_percentile.value | 0.93716632 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |