Beyond CRISPR: seekRNA offers a new path for precise gene editing

Scientists at the University of Sydney have developed a gene-editing tool with greater accuracy and flexibility than the industry standard CRISPR, revolutionizing genetic engineering in medicine, agriculture and biotechnology.

SeekRNA uses a programmable ribonucleic acid (RNA) strand that can instantly identify sites for insertion into genetic sequences, simplifying the editing process and reducing errors.

The new gene editing tool is being developed by a team led by Dr. Sandro Ataide from the School of Life and Environmental Sciences. Their findings have been published in Nature communication.

“We are extremely excited about the potential of this technology. 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,” said Dr. Ataide.

“With CRISPR you need additional components to have a cut-and-paste tool, while the promise of seekRNA is that it is a standalone cut-and-paste tool with higher accuracy that can cover a wide range of possibilities can offer. DNA sequences.”

CRISPR relies on creating a break in both strands of the target DNA, the double-helix genetic code of life, and requires other proteins or the DNA repair machinery to insert the new DNA sequence. This can introduce errors.

Dr. Ataide said: “SeekRNA can precisely cleave the target site and insert the new DNA sequence without the use of other proteins. This provides a much cleaner editing tool with higher accuracy and fewer errors.”

Gene editing has opened up completely new areas of research and application since the development of CRISPR more than ten years ago. It has led to improvements in disease resistance in fruits and crops, reduced the cost and speed of human disease detection, aided the search for a cure for sickle cell disease, and enabled the development of a revolutionary cancer treatment known is known as (CAR) T-cell therapy.

“We are just scratching the surface of what gene editing can do. We hope that by developing this new approach to gene editing we can contribute to advances in healthcare, agriculture and biotechnology,” said co-author professor Ruth Hall of the university. from Sydney.

Accurate genetic targeting

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, but these families exhibit high target specificity.

It is this accuracy that seekRNA has used to achieve promising results so far. Using the accuracy of this insertion sequence family, seekRNA can be tailored to any genomic sequence and insert the new DNA in a precise orientation.

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

An advantage of the system reported in this study is that it can be applied with only a single protein of modest size plus a short seekRNA strand, to efficiently move genetic cargo. SeekRNA consists 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 packaged into nanoscale biological delivery vehicles (vesicles or lipid nanoparticles) for delivery to cells of interest.

Direct insertion into DNA

Another point of differentiation is this technology’s ability to self-insert DNA sequences at the desired location, 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 University of Sydney research associate Rezwan Siddiquee, lead author of the paper. “This limits the scope.”

Other teams worldwide are conducting similar research into the gene editing potential of the IS1111 and IS110 families. Dr. However, Ataide says they have only shown results for one member of the IS110 family and rely on a much larger RNA version. The team in Sydney is advancing its technique through direct laboratory sampling and application of the shorter seekRNA itself.