ArticleFrontiers in molecular biosciences2020
Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.
Article in Frontiers in molecular biosciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants.Frontiers in plant science · 2020Pooled it
- ARROW: Allele-Specific Recombined gRNA Design for Reduced Off-Target with Enhanced Specificity.Bioengineering (Basel, Switzerland) · 2025Article
- Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR-Cas9 off-target activity.NAR genomics and bioinformatics · 2025Article
- Graph theory approaches for molecular dynamics simulations.Quarterly reviews of biophysics · 2024Article
- Crispr-SGRU: Prediction of CRISPR/Cas9 Off-Target Activities with Mismatches and Indels Using Stacked BiGRU.International journal of molecular sciences · 2024Article
- Hybrid Multitask Learning Reveals Sequence Features Driving Specificity in the CRISPR/Cas9 System.Biomolecules · 2023Article
- The Electronic Structure of Genome Editors from the First Principles.Electronic structure (Bristol, England) · 2023Article
- Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations.ACS omega · 2023Review
- Editorial: RNAs at the crossroads between effectors and targets; discovery and development of new drugs.Frontiers in molecular biosciences · 2023Article
- Deciphering the QR Code of the CRISPR-Cas9 System: Synergy between Gln768 (Q) and Arg976 (R).ACS physical chemistry Au · 2022Article
- Article
- A Machine Learning Approach to Identify the Importance of Novel Features for CRISPR/Cas9 Activity Prediction.Biomolecules · 2022Article
- Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods.Current opinion in structural biology · 2022Review
- Searching for Low Probability Opening Events in a DNA Sliding Clamp.Life (Basel, Switzerland) · 2022Article
- Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes.Frontiers in molecular biosciences · 2022Review
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Article
- Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.Frontiers in molecular biosciences · 2021Article
- Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed byACS catalysis · 2020Article
- Establishing the allosteric mechanism in CRISPR-Cas9.Wiley interdisciplinary reviews. Computational molecular scienceArticle
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects.
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Registered trials
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