HKUST Creates World's First DNA-Guided CRISPR Gene Editing Tool

Flipping the CRISPR Script

Researchers at the Hong Kong University of Science and Technology (HKUST) have unveiled what they describe as the world's first DNA-guided CRISPR-Cas system capable of programmable RNA targeting and cleavage. The findings, published in Nature Biotechnology on 1 May, invert the traditional CRISPR paradigm, which normally uses RNA guides to direct proteins towards DNA targets.

The research team, led by Professor Hsing I-Ming of HKUST's Department of Chemical and Biological Engineering, working with Associate Professor Zhai Yuanliang of the Division of Life Science, engineered a synthetic CRISPR DNA molecule, dubbed crDNA, that reprograms the Cas12a protein to use DNA as a guide for targeting RNA. The team decoupled two functions normally fused in nature - the activation signal known as the PAM sequence and the information-carrying address - producing a functional deoxyribonucleoprotein complex.

Why DNA Guides Matter

Using synthetic DNA guides offers significant practical advantages over RNA. DNA is chemically more stable, cheaper to synthesise, and does not require cold-chain storage. That makes the new system well-suited for deployment in clinics, airports, and resource-limited settings where keeping reagents refrigerated is difficult or impossible.

SLEUTH Diagnostic Platform

Building on the mechanism, the team constructed a diagnostic platform called SLEUTH, short for Specific Locus Evaluation Utilizing Targeted Hydrolysis. The one-pot assay couples isothermal amplification with DNA-guided Cas12a readout, achieving attomolar-level sensitivity and 100% concordance with RT-qPCR across 31 clinical SARS-CoV-2 samples.

The platform also demonstrated approximately 76% mRNA knockdown in human cells with minimal off-target effects confirmed by RNA sequencing. Compared to the existing RNA-targeting tool Cas13, the DNA-guided Cas12a system produces fewer collateral RNA cleavage effects - a safety advantage for therapeutic development.

Future Applications

HKUST has filed two U.S. provisional patents and is exploring applications in antiviral therapies, live-cell RNA imaging, and programmable RNA regulation. Over the next three years, the team plans to expand SLEUTH to detect other respiratory viruses and investigate liquid biopsy applications for identifying circulating RNA biomarkers in cancer, opening up potential early detection routes for diseases that currently rely on invasive testing.