Broken String Biosciences’ INDUCE-seq platform demonstrates impact of structural DNA changes on specificity of CRISPR-Cas9 gene editing

  • Research published in Molecular Cell used INDUCE-seq to identify DNA topology as an important regulator of CRISPR targeting specificity
  • Peer-reviewed data demonstrates the sensitivity of INDUCE-seq DNA break mapping platform, in identifying topology-related off-target events across the genome in cells


Cambridge, UK, 18 October 2023: Broken String Biosciences (“Broken String”), a genomics company building a technology platform to drive the development of cell and gene therapies that are safer by design, today announced that its INDUCE-seq™ DNA break-mapping technology had been used in a peer-reviewed research paper to characterize off-target effects of CRISPR-Cas9 gene editing resulting from changes in DNA topology1. Published in Molecular Cell, the research highlights DNA topology as a key regulator to CRISPR targeting specificity that must be carefully considered during development of CRISPR-based therapies.

Since its discovery, the CRISPR-Cas9 system has enabled researchers to elicit precise DNA edits at virtually any site across the genome. However, the full potential of this system as a clinical tool has been constrained by off-target effects.

The new study was co-authored by a team of scientists, including Broken String co-founders Professor Simon Reed and Patrick van Eijk, PhD. As part of the research, the team analyzed the impact of alterations to DNA structure, in the form of negative supercoiling, on off-target effects of Cas9. Using an adapted cell-free off-target measuring approach, the team identified that negative supercoiling induced up to 10,000 genome-wide off-target events that were formed as a result of increased mismatch tolerance. INDUCE-seq confirmed these findings in gene edited cells, demonstrating that sites of increased superhelical torsion were more susceptible to off-target induction in live cells.

Professor Simon Reed, Chief Scientific Officer, Broken String Biosciences, remarked: "This study demonstrates the importance of measuring off-target gene editing activity directly in the cells that are being edited. Evidently, there are factors affecting off-target activity in cells, such as superhelical torsion in the DNA structure, that cannot be predicted in silico using DNA sequence analysis alone."

  1. Newton, M.D. et al. (2023) ‘Negative DNA supercoiling induces genome-wide cas9 off-target activity’, Molecular Cell, 83(19). doi:10.1016/j.molcel.2023.09.008.

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About Broken String Biosciences

Broken String Biosciences is a genomics company with the goal of developing safer cell and gene therapies by assessing the stability of the genome. The Company is building a technology platform pipeline that will drive the development of cell and gene therapies that are safer by design. Its core technology, INDUCE-seq™, is a Next Generation Sequencing (NGS)-based DNA break mapping platform that enables companies developing cell and gene therapies to measure and quantify the specificity of off-target genetic edits and to evaluate the associated genetic outcomes. The platform technology provides data-driven, actionable insights across the discovery, pre-clinical and clinical development stages to unlock new therapeutic targets within the genome and to advance gene editing programs.

Broken String Biosciences was spun out of Cardiff University in 2020 and completed a six-month residency at the Illumina Accelerator in Cambridge, UK. The Company has raised financing of c.$20m USD to date from venture capital investors.

Broken String Biosciences has established strong links with several academic and industrial collaborators and is headquartered at the BioData Innovation Centre, Wellcome Genome Campus, Cambridge, UK, with laboratory premises nearby at Chesterford Research Park.

To find out more, visit:, follow Broken String Biosciences on LinkedIn, and @BrokenStringBio on Twitter.

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