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PNP Editing: The New Kid on the Gene-Editing Block

Emerging Technologies
August 25, 2023

Optimizing the precision of gene-editing tools is a top priority for researchers. A breakthrough technique from KAUST stands out in the gene-editing arena, blending two innovative molecular technologies to achieve enhanced delivery, specificity, and targeting.

Introducing PNP Editing: The Blend of PNAs and pAgos

In the vast ocean of genome-editing techniques, PNP editing is making waves. This revolutionary method hinges on the integration of peptide nucleic acids (PNAs) – a unique family of DNA-like molecules—and prokaryotic Argonautes (pAgos)—a specific kind of DNA-slicing enzyme. More details can be found through investigators' recently published work in Nucleic Acids Research.

Here's how it works: The PNAs cleverly unzip and find their way into the DNA helix. Following their lead, pAgos, directed by bite-sized genetic fragments, clutch onto the relaxed helix, specifically targeting and nicking both strands of the DNA.

Why PNP Editing is a Game-Changer in the Gene-Editing Landscape

At a glance, PNP editing might seem like another tool in the gene-editing toolkit. But its uniqueness lies in its nuanced approach and benefits:

  • Range & Precision: PNP editing, in essence, can be utilized at a broader array of sites within the genome. It creates accurate breaks in the double-stranded DNA, slashing the chances of off-target activities, a concern in terms of safety.
  • Compact & Deliverable: The minuscule size of the tool's components offers an edge in packaging and shipping the gene-editing mechanism right to its desired destination. This means it can potentially reach the mitochondria—our cells' energy powerhouses—and other cellular organelles.

According to Magdy Mahfouz, the KAUST bioengineer at the helm of the study, “The technology we built significantly improves the efficiency and the activity of programmable double-strand breaks that could be used for gene editing.”

Mahfouz and team left no stone unturned in their research. Their exhaustive exploration spanned a wide gamut: from experimenting with different PNAs, pAgo proteins, and guide molecules to testing under varied conditions. And the results? PNP editing emerged as a versatile platform for specific gene manipulations across DNA materials.

“Programmable site-specific nucleases promise to unlock myriad applications in basic biology research, biotechnology, and gene therapy,” the authors wrote. “Gene-editing systems have revolutionized our ability to engineer genomes across diverse eukaryotic species. However, key challenges, including delivery, specificity, and targeting organellar genomes, pose barriers to translational applications.”

The study authors continued, stating that “we used PNAs to facilitate precise DNA strand invasion and unwinding, enabling pAgo proteins to specifically bind displaced single-stranded DNA and introduce site-specific double-strand breaks (DSBs) independent of the target sequence. Our design allows the simultaneous use of multiple PNP editors to generate multiple site-specific DSBs, thereby informing design considerations for potential in vitro and in vivo applications, including genome editing.”

What's Next for PNP Editing?

While the PNP editing technique showcases immense promise, there's more work ahead. Tin Marsic, a PhD candidate in Mahfouz’s team, emphasized the upcoming challenges: “We need to optimize delivery and demonstrate robust in vivo activity—both in cell-culture experiments and in animal models of disease.”

The next vital step would involve contrasting the performance of PNP editing directly against the stalwart CRISPR-based methods. However, Marsic assures that the data collected thus far indicates their concept’s versatility.

With the combined prowess of PNAs' targeted strand invasion and the precise slicing capability of pAgos, PNP editing could potentially reshape fields like precision medicine, agriculture, and core scientific research.

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