New Study Shows the Impact of Structural DNA Changes on CRISPR-Cas9 Gene Editing


A recent study published in Molecular Cell by Broken String Biosciences has shed light on the impact of structural DNA changes on the specificity of CRISPR-Cas9 gene editing. The study utilized Broken String’s INDUCE-seq DNA break-mapping technology to characterize the off-target effects of CRISPR-Cas9 gene editing resulting from changes in DNA topology.

The CRISPR-Cas9 system has revolutionized gene editing by allowing researchers to make precise DNA edits. However, one of the challenges faced by this system is the occurrence of off-target effects, where unintended changes are made to the genome. This study aimed to understand the role of DNA topology in regulating the specificity of CRISPR targeting, which is crucial for the development of safe and effective CRISPR-based therapies.

The research was co-authored by Professor Simon Reed and Patrick van Eijk, PhD, who are co-founders of Broken String. The team focused on analyzing the impact of alterations to DNA structure, specifically negative supercoiling, on the off-target effects of Cas9. Negative supercoiling refers to the twisting of the DNA molecule in the opposite direction of its natural coiling.

Using an adapted cell-free off-target measuring approach, the team discovered that negative supercoiling induced up to 10,000 genome-wide off-target events, resulting from increased mismatch tolerance. This means that the changes in DNA topology made the system more prone to making unintended edits. To confirm these findings in gene-edited cells, the team employed Broken String’s INDUCE-seq technology, which confirmed that sites with increased superhelical torsion were more susceptible to off-target induction in live cells.

This research highlights the importance of considering DNA topology in the development of CRISPR-based therapies. By understanding how changes in DNA structure can affect the specificity of gene editing, researchers can work towards minimizing off-target effects and making these therapies safer.

Broken String Biosciences’ INDUCE-seq technology offers a powerful tool for characterizing off-target effects and understanding the impact of structural DNA changes on CRISPR-Cas9 gene editing. This technology enables researchers to map DNA breaks and analyze the effects of alterations in DNA topology on gene editing specificity. By providing valuable insights into off-target effects, INDUCE-seq can contribute to the development of safer and more precise CRISPR-based therapies.

In conclusion, this study by Broken String Biosciences emphasizes the need to consider DNA topology when developing CRISPR-based therapies. The findings of this research shed light on the impact of structural DNA changes on the specificity of gene editing, providing valuable insights for the improvement of CRISPR technologies. By addressing the issue of off-target effects, researchers can make gene and cell therapies safer and more effective.


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