Surpassing CRISPR: How SeekRNA Is Redefining the Future of Gene Editing

The University of Sydney introduces SeekRNA, a gene-editing tool superior to CRISPR, offering direct DNA insertion with high precision. This innovation promises significant advancements in genetic engineering by enabling cleaner and more accurate edits, with potential applications across various fields including health and agriculture.

SeekRNA enhances gene editing with greater precision and simpler application than CRISPR, promising broader and more effective genetic interventions.

Researchers from the <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

University of Sydney

The University of Sydney is a public research university located in Sydney, New South Wales, Australia. Founded in 1850, it is the oldest university in Australia and is consistently ranked among the top universities in the world. The University of Sydney has a strong focus on research and offers a wide range of undergraduate and postgraduate programs across a variety of disciplines, including arts, business, engineering, law, medicine, and science.

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>University of Sydney have developed a new gene-editing tool, SeekRNA, which promises greater <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

accuracy

How close the measured value conforms to the correct value.

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>accuracy and flexibility than CRISPR. SeekRNA uses a programmable ribonucleic <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

acid

Any substance that when dissolved in water, gives a pH less than 7.0, or donates a hydrogen ion.

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>acid (<span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

RNA

Ribonucleic acid (RNA) is a polymeric molecule similar to DNA that is essential in various biological roles in coding, decoding, regulation and expression of genes. Both are nucleic acids, but unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups. Attached to each sugar is one of four bases—adenine (A), uracil (U), cytosine (C), or guanine (G). Different types of RNA exist in the cell: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA).

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>RNA) strand that can directly identify sites for insertion in genetic sequences, simplifying the editing process and reducing errors. This technology, detailed in <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

Nature Communications

<em>Nature Communications</em> is an open-access, peer-reviewed journal that publishes high-quality research from all areas of the natural sciences, including physics, chemistry, Earth sciences, and biology. The journal is part of the Nature Publishing Group and was launched in 2010. "Nature Communications" aims to facilitate the rapid dissemination of important research findings and to foster multidisciplinary collaboration and communication among scientists.

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>Nature Communications, could revolutionize medicine, agriculture, and biotechnology by allowing for precise genetic modifications.

Advantages Over CRISPR

“We are tremendously excited by the potential for 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,” research lead Dr Sandro Ataide said.

“With CRISPR you need extra components to have a ‘cut-and-paste tool’, whereas the promise of seekRNA is that it is a stand-alone ‘cut-and-paste tool’ with higher accuracy that can deliver a wide range of <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

DNA

DNA, or deoxyribonucleic acid, is a molecule composed of two long strands of nucleotides that coil around each other to form a double helix. It is the hereditary material in humans and almost all other organisms that carries genetic instructions for development, functioning, growth, and reproduction. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA).

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>DNA sequences.”

Dr Sandro Ataide and Team in the Laboratory

Dr Sandro Ataide (left) with lead author Rezwan Siddiquee and Caitlin McCormack in the Ataide Laboratory at the University of Sydney. Credit: Fiona Wolf/University of Sydney

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

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

Applications and Potential

Since the development of CRISPR more than 10 years ago, gene editing has opened new research and application areas. It has led to improvements in disease resistance in fruit and crops, reduced the cost and speed of human disease detection, helped in the search for a cure for sickle cell disease, and allowed for the development of a revolutionary cancer treatment known as (CAR) T-cell therapy.

Dr Sandro Ataide from the School of Life and Environmental Sciences in the Faculty of Science at the University of Sydney. Credit: Fiona Wolf/University of Sydney

“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 joint author Professor Ruth Hall from the University of Sydney.

Technical Breakthroughs and Future Prospects

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.

Dr Sandro Ataide in the Ataide Laboratory at the School of Life and Environmental Sciences at the University of Sydney. Credit: Fiona Wolf/University of Sydney

Using the accuracy from this insertion sequence family, seekRNA 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. Our next steps will be to investigate if the technology can be adapted for the more complex eukaryotic cells found in humans,” Ataide said.

Novel Delivery Systems

An advantage of the system reported in this study 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 <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

amino acids

<div class="cell text-container large-6 small-order-0 large-order-1">
<div class="text-wrapper"><br />Amino acids are a set of organic compounds used to build proteins. There are about 500 naturally occurring known amino acids, though only 20 appear in the genetic code. Proteins consist of one or more chains of amino acids called polypeptides. The sequence of the amino acid chain causes the polypeptide to fold into a shape that is biologically active. The amino acid sequences of proteins are encoded in the genes. Nine proteinogenic amino acids are called "essential" for humans because they cannot be produced from other compounds by the human body and so must be taken in as food.<br /></div>
</div>

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>amino acids and an RNA strand of between 70 and 100 nucleotides. A system of this size could be packed into biological <span class="glossaryLink" aria-describedby="tt" data-cmtooltip="

nanoscale

The term "nanoscale" refers to dimensions that are measured in nanometers (nm), with one nanometer equaling one-billionth of a meter. This scale encompasses sizes from approximately 1 to 100 nanometers, where unique physical, chemical, and biological properties emerge that are not present in bulk materials. At the nanoscale, materials exhibit phenomena such as quantum effects and increased surface area to volume ratios, which can significantly alter their optical, electrical, and magnetic behaviors. These characteristics make nanoscale materials highly valuable for a wide range of applications, including electronics, medicine, and materials science.

” data-gt-translate-attributes=”[{"attribute":"data-cmtooltip", "format":"html"}]” tabindex=”0″ role=”link”>nanoscale delivery vehicles (vesicles or lipid nanoparticles) for delivery to cells of interest.

Dr Sandro Ataide from the School of Life and Environmental Sciences in the Faculty of Science at the University of Sydney. Credit: Fiona Wolf/University of Sydney

Overcoming CRISPR Limitations

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 University of Sydney research associate Rezwan Siddiquee, lead author of the paper. “This restricts the scope of application.”

International Research Context

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

Reference: “A programmable seekRNA guides target selection by IS1111 and IS110 type insertion sequences” by Rezwan Siddiquee, Carol H. Pong, Ruth M. Hall and Sandro F. Ataide, 19 June 2024, Nature Communications.
DOI: 10.1038/s41467-024-49474-9

Dr Sandro Ataide, Professor Ruth Hall, and Rezwan Siddiquee are inventors of patent applications related to this work. The research was supported by the University of Sydney Deputy Vice-Chancellor (Research) Strategic Research Impact Fund and a National Health and Medical Research Council (NHMRC) Investigator grant.

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