Enhancing CRISPR/Cas‐Mediated Gene Knockout With Short Non‐Homologous Oligonucleotides

Chew, Yen Peng and Ferenczi, Áron and Dannay, Marie and Ponce‐Lilly, Cristina and Kovac, Adam and Tóth, Dávid and Tóth, Szilvia Zita and Molnár, Attila (2026) Enhancing CRISPR/Cas‐Mediated Gene Knockout With Short Non‐Homologous Oligonucleotides. PLANT BIOTECHNOLOGY JOURNAL, 24. pp. 3742-3753. ISSN 1467-7644 (print); 1467-7652 (online)

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Abstract

Chlamydomonas reinhardtii is a model green microalga that has great industrial potential as a sustainable bio‐factory for recombinant protein and high‐value chemical production. Efficient genome editing tools are required to redesign this organism for synthetic biology applications. CRISPR‐Cas editing technologies have already been adapted for gene knockout, transgene knock‐in, and precise gene editing in C. reinhardtii . However, the efficacy of CRISPR/Cas‐mediated gene knockout (KO) is low, which hampers pathway engineering and functional genomic studies. Here we report that co‐delivery of CRISPR‐Cas gene editing reagents with short double‐stranded non‐homologous oligodeoxynucleotides (dsNHO) increases gene knockout efficacy up to 100‐fold in C. reinhardtii . This phenomenon, referred to as non‐homologous oligonucleotide enhancement (NOE), is heavily affected by the length, structure, and chemical modifications of dsNHO, and is largely mediated by the DNA double‐stranded break sensor KU70/80 (KU) heterodimer in a Cas nuclease‐, locus‐, and strain‐independent manner. Our data suggest that dsNHOs disrupt the cell's double‐stranded break (DSB) sensing pathways, consequently shifting the balance of DNA repair from canonical non‐homologous end joining (c‐NHEJ) towards the more error‐prone, microhomology‐mediated end joining (MMEJ), which could be harnessed as a strategy for improving gene KO efficiency in Chlamydomonas and beyond.

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