ContactSeek uses AlphaFold3 to improve DNA base editing precision
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Researchers developed ContactSeek, an AI framework leveraging AlphaFold3-predicted contact probability to enhance specificity of adenine base editors. The best variant, combining two mutations in Cas9 and TadA8e, outperformed several known high-fidelity editors in targeted amplicon sequencing and genome-wide profiling. The approach also generalized to Cas12a-based cytosine base editors.
The Framework
ContactSeek uses AlphaFold3 (AF3)-predicted contact probability to improve specificity of genome editors, using Cas9–TadA adenine base editors as a demonstration. The team mapped genome-wide off-targets and fed off-target DNA sequences to AF3, finding contact probability more sensitive than predicted 3D structures for detecting differential interactions. ContactSeek identified and ranked consensus contact regions—neighbouring Cas residues with consistent contact changes to DNA/guide RNA—and pinpointed specificity-determining residues within them.
Validation Results
Targeted amplicon sequencing, genome-wide profiling, R-loop assay and RNA-sequencing confirmed greatly enhanced specificity. The best variant, combining two mutations of Cas9 and TadA8e, outperformed several known high-fidelity adenine base editors. ContactSeek also generalized to Cas12a-based cytosine base editors, demonstrating modular applicability.
Data and Availability
AF3 prediction outputs and targeted amplicon sequencing raw count tables are deposited at Zenodo (DOI: 10.5281/zenodo.17197986 and 10.5281/zenodo.17243125). Raw dI-profiling sequencing data are in the Genome Sequence Archive under accession codes HRA013626 and HRA013767 (BioProject PRJCA046878). RNA-seq data for off-target assessments were downloaded from SRA under PRJNA938578 and PRJNA811343.
What's Next
The framework may be extended to other editor types and therapeutic applications. It remains unclear how ContactSeek will perform in in vivo models or clinical settings.
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ContactSeek uses AlphaFold3 to improve DNA base editing precision
