ArticleScience advances2020
DNB-based on-chip motif finding: A high-throughput method to profile different types of protein-DNA interactions.
Article in Science advances, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Discovery and engineering of a new BvCas12a nuclease for mammalian genome editing and nucleic acid detection.Science China. Life sciences · 2026Article
- Multiplexed single-molecule characterization at the library scale.Nature protocols · 2026Review
- Fast, cost-effective and flexible DNA sequencing by roll-to-roll fluidics.Nature methods · 2025Article
- Systematic discovery of DNA-binding tandem repeat proteins.Nucleic acids research · 2024Article
- Article
- High-throughput biochemistry in RNA sequence space: predicting structure and function.Nature reviews. Genetics · 2023Review
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we report a sensitive DocMF system that uses next-generation sequencing chips to profile protein-DNA interactions. Using DocMF, we successfully identified a variety of endonuclease recognition sites and the protospacer adjacent motif (PAM) sequences of different CRISPR systems. DocMF can simultaneously screen both 5' and 3' PAMs with high coverage. For SpCas9, we found noncanonical 5'-NAG-3' (~5%) and 5'-NGA-3' (~1.6%), in addition to its common PAMs, 5'-NGG-3' (~89.9%). More relaxed PAM sequences of two uncharacterized Cas endonucleases, VeCas9 and BvCas12a, were extensively characterized using DocMF. Moreover, we observed that dCas9, a DNA binding protein lacking endonuclease activity, preferably bound to the previously reported 5'-NGG-3' sequence. In summary, our studies demonstrate that DocMF is the first tool with the capacity to exhaustively assay both the binding and the cutting properties of different DNA binding proteins.
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Registered trials
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