seekRNA brings a new way for precise gene editing

University of Sydney scientists have developed a gene-editing tool with greater precision and flexibility than the industry standard CRISPR, which has revolutionized genetic engineering in medicine, agriculture and biotechnology.

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

A new gene editing tool is being developed by a team led by Dr. Sandro Ataidem at the School of Life and Environmental Sciences. Their findings were published in The nature of 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 that overcomes the limitations of current technologies,” said Dr. Ataide.

“With CRISPR, you need additional components to have a ‘cut-and-paste tool,’ whereas the promise of seekRNA is that it is a separate, higher-precision ‘cut-and-paste tool’ that can provide a wide range of DNA sequences.”

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

Dr. Ataide said, “SeekRNA can precisely cleave the target site and insert the new DNA sequence without using any other proteins. This allows for a much cleaner editing tool with higher accuracy and fewer errors.”

Gene-editing has opened up entirely new areas of research and application since the development of CRISPR more than 10 years ago. It has led to improved disease resistance in fruits and crops, reduced the cost and speed of detecting human diseases, aided in the search for a cure for sickle cell disease, and enabled the development of a revolutionary cancer treatment known as (CAR) T-cell therapy.

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

Precise 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 show little or no target selectivity, but these families show high target specificity.

It’s this precision that seekRNA has used to achieve its promising results so far. Using the precision from this family of insertion sequences, seekRNA can be modified to any genomic sequence and insert new DNA in a precise orientation.

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

The advantage of the system presented in this study is that it can be used using only a single protein of modest size plus a short chain of seekRNA for efficient transfer of genetic cargo. SeekRNA consists of a small protein of 350 amino acids and an RNA chain of 70 to 100 nucleotides in length.

A system of this size could be packaged into biological nanoscale transport carriers (vesicles or lipid nanoparticles) for delivery to cells of interest.

Direct insertion into DNA

Another difference is the ability of this technology to automatically insert DNA sequences into the desired location, which is 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 researcher Rezwan Siddiquee, lead author of the paper. “That limits the range of use.”

Globally, other teams are conducting similar research into the gene editing potential of the IS1111 and IS110 families. Dr. However, Ataide says they only showed results for one member of the IS110 family and rely on a much larger version of the RNA. The team in Sydney is perfecting their technique by direct laboratory sampling and application of the shorter seekRNA itself.