Append Editing Offers New Strategy for DNA Modification

Bacterial enzymes inspire genome engineering technique

Scientists from the Helmholtz Institute for RNA-based Infection Research (HIRI) and collaborating institutions have developed a DNA-editing method that introduces small chemical modifications at specific sites in the genome. The technique, described in Nature Biotechnology, is based on bacterial enzymes used in their natural defense systems and has been shown to work differently depending on the target organism.

A chemical alternative to cutting DNA

Recent developments in genome editing have moved toward techniques that minimize DNA damage. CRISPR-Cas9, which slices DNA at targeted locations, has been adapted into several forms that perform more precise operations, such as base editing. These methods allow researchers to make small changes to the genome without creating breaks in the DNA.

The new technique, named "append editing" by the authors, is based on a system used by bacteria to defend against viruses. When bacteria detect viral infection, they use an enzyme called DarT2 to add a chemical group—ADP-ribose—to the viral DNA. This modification blocks the virus from replicating. When the threat subsides, a second enzyme, DarG, removes the ADP-ribose tag.

By adapting this mechanism, the researchers created a programmable method for modifying DNA without removing or replacing genetic material. Instead, they append a chemical group at a defined site in the genome, similar to adding a marker rather than editing the DNA code directly.

Different results in bacteria and eukaryotes

When the team tested this technique in different organisms, they found that it led to distinct outcomes. In bacteria, append editing promoted the integration of large genetic segments based on a supplied template. In contrast, when applied to eukaryotic cells—including fungi, plants and human cells—it triggered a base change at the tagged DNA site.

This contrast suggests that the DNA repair processes triggered by append editing vary between organisms. These findings offer a new approach for tailoring genome editing tools to the biology of specific systems.

Future research directions

Although the work shows promise, append editing remains in the early stages of development. Researchers suggest that further studies will be needed to optimize the technique and understand how cells respond to the appended chemical tags.

Potential applications could include modifying beneficial microbes, studying pathogens and exploring DNA repair mechanisms in human cells. However, clinical applications are not imminent, and the method has not yet been tested in animals or human tissues beyond cell culture.

Reference: Gupta D, Patinios C, Bassett HV, et al. Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes. Nat Biotechnol. 2025; doi:10.1038/s41587-025-02802-w

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