ArticleNature structural & molecular biology2023
The energy landscape for R-loop formation by the CRISPR-Cas Cascade complex.
Article in Nature structural & molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Structural insight into IscB's RNA-lid-based inactivation mechanism.Nature structural & molecular biology · 2026Article
- RNA-DNA hybrid binding domain broadens the editing window of base editors.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Article
- Structural and mechanistic insights into the sequential dsDNA cleavage by SpCas12f1.Nucleic acids research · 2025Article
- Dynamic basis of supercoiling-dependent DNA interrogation by Cas12a via R-loop intermediates.Nature communications · 2025Article
- Short-range translocation by a restriction enzyme motor triggers diffusion along DNA.Nature chemical biology · 2024Article
- Retention of the RNA ends provides the molecular memory for maintaining the activation of the Csm complex.Nucleic acids research · 2024Article
- Heavy Metal Stabilization of DNA Origami Nanostructures.Nano letters · 2024Article
- Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system.Nature communications · 2023Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) sequences and CRISPR-associated (Cas) genes comprise CIRSPR-Cas effector complexes, which have revolutionized gene editing with their ability to target specific genomic loci using CRISPR RNA (crRNA) complementarity. Recognition of double-stranded DNA targets proceeds via DNA unwinding and base pairing between crRNA and the DNA target strand, forming an R-loop structure. Full R-loop extension is a prerequisite for subsequent DNA cleavage. However, the recognition of unintended sequences with multiple mismatches has limited therapeutic applications and is still poorly understood on a mechanistic level. Here we set up ultrafast DNA unwinding experiments on the basis of plasmonic DNA origami nanorotors to study R-loop formation by the Cascade effector complex in real time, close to base-pair resolution. We resolve a weak global downhill bias of the forming R-loop, followed by a steep uphill bias for the final base pairs. We also show that the energy landscape is modulated by base flips and mismatches. These findings suggest that Cascade-mediated R-loop formation occurs on short timescales in submillisecond single base-pair steps, but on longer timescales in six base-pair intermediate steps, in agreement with the structural periodicity of the crRNA-DNA hybrid.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.