SeekRNA offers a new pathway for accurate gene editing

Scientists at The University of Sydney have developed a gene-editing tool that is claimed to have greater accuracy and flexibility than the industry standard, CRISPR. It has been described in the journal Nature Communications.

While CRISPR has revolutionised genetic engineering in medicine, agriculture and biotechnology, the technique relies on creating a break in both strands of target DNA and requires other proteins or the DNA repair machinery to insert the new DNA sequence. This can introduce errors.

SeekRNA, on the other hand, uses a programmable RNA strand that can directly identify sites for insertion in genetic sequences. This means it can “precisely cleave the target site and insert the new DNA sequence without the use of any other proteins”, noted team leader Dr Sandro Ataide, which “allows for a much cleaner editing tool with higher accuracy and fewer errors”.

SeekRNA is derived from a family of naturally occurring insertion sequences known as IS1111 and IS110, discovered in bacteria and archaea (cells without a nucleus). Most insertion sequence proteins exhibit little or no target selectivity; however, these families exhibit high target specificity. It is this accuracy that seekRNA has used to achieve its promising results to date, as it means the tool can be modified to any genomic sequence and insert the new DNA in a precise orientation.

“In the laboratory we have successfully tested seekRNA in bacteria,” Ataide said. “Our next steps will be to investigate if the technology can be adapted for the more complex eukaryotic cells found in humans.”

An advantage of the new system is that it can be applied using only a single protein of modest size plus a short seekRNA strand, to efficiently move genetic cargo. SeekRNA is made up of a small protein of 350 amino acids and an RNA strand of between 70 and 100 nucleotides; a system of this size could be packed into biological nanoscale delivery vehicles (vesicles or lipid nanoparticles) for delivery to cells of interest. Another point of differentiation is this technology’s ability to insert DNA sequences in the desired location by itself, a feat not possible with many current editing tools.

“Current CRISPR technology has limitations on the size of genetic sequences that can be introduced,” said research associate Rezwan Siddiquee, lead author of the paper. “This restricts the scope of application.”

Globally, other teams are pursuing similar research into the gene-editing potential of the IS1111 and IS110 family; however, they have only have shown results for one member of the IS110 family and rely on a much larger RNA version. The Sydney team is advancing its technique through direct laboratory sampling and application of the shorter seekRNA itself.

“We are tremendously excited by the potential for this technology,” Ataide said. “SeekRNA’s ability to target selection with precision and flexibility sets the stage for a new era of genetic engineering, surpassing the limitations of current technologies.”

“We are very much in the early days of what gene editing can do,” added joint author Professor Ruth Hall. “We hope that by developing this new approach to gene editing, we can contribute to advances in health, agriculture and biotechnology.”

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