Dannie Pengin Beijing

Published: 10 Aug 2025

A group of Chinese scientists has overcome a challenge that stumped biologists for decades by developing a new gene-editing tool that can precisely manipulate millions of base pairs – the building blocks of DNA.

The innovation has been hailed as “very significant progress” by Professor Yin Hao, a gene editing specialist at Wuhan University’s medical research institute, who was not involved in the study. He added that it would help lay the foundation for future advances in genetic engineering in biomedicine and agriculture.

A single human cell contains around 3 billion base pairs. Well-known technologies such as Crispr are widely used for the precise editing of specific genes and nucleic acid bases. However, biologists have struggled to scale up the process to precisely manipulate thousands or even millions of bases.

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Now, a team led by Gao Caixia – a principal investigator at the Institute of Genetics and Developmental Biology at the Chinese Academy of Sciences in Beijing – has solved the riddle by making the decade-old gene editing tool much easier to use and more efficient. The study was published by the peer-reviewed journal Cell on Monday.

The new genome editing technologies, collectively known as programmable chromosome engineering (PCE) systems, can edit large DNA fragments with precision by “handling bases ranging from the thousands to the millions in higher organisms, especially plants”, according to the institute.

The toolset holds promise for transforming the way scientists conduct research in emerging fields such as agricultural seed cultivation and synthetic biology.

According to a CAS branch institute in Beijing, by manipulating genomic structural variation, the technology will “open up new avenues for crop trait improvement and genetic disease treatment”.

The advance could also accelerate the development of artificial chromosomes, which have promising applications in emerging fields such as synthetic biology.

Yin said the story began with Cre-Lox – a crucial and fundamental enzyme in biomedicine that is used for inserting, inverting and replacing large segments of DNA, as well as other edits.

But since its discovery in the 1980s, the enzyme’s many drawbacks have deterred scientists from using it. One of the problems has been its poor efficiency, which decreases as the size of the fragment being edited increases. Cre-Lox also leaves “scars” behind.

Yin added that because the edited DNA sequences were reversible, the changes were likely only temporary, even after scientists had gone to great lengths to achieve a desired manipulation.

This is where Gao – whose lab has focused on developing and applying genome editing technologies, particularly in agriculture – and her team are making a contribution.

By redesigning and optimising editing strategies, the research team addressed each of the challenges and developed new methods to advance the technology.

The PCE technique enables precise manipulation of DNA fragments that is 3½ times more efficient than the original enzyme editor with no scarring, while minimising the possibility of reversal.

“This is very significant progress,” Yin said. In the past, it might have been necessary to edit 1,000 seeds to select one that met the requirements, he said, adding that with the new tool, that number could be reduced to 100, which “greatly reduces the workload of researchers”.

“Over the past four decades, this may be a very rare, even unprecedented, case of successfully modifying this enzyme to enhance its capabilities as a commonly used gene editing tool,” Yin said.

He said he expected that PCE systems would eventually replace existing Cre-Lox systems in laboratories around the world, bringing new efficiencies to medical research and agricultural engineering.

Dannie Peng

Dannie joined SCMP in 2023 and focuses on science stories in China, with a particular interest in the scientific community and societal impacts of scientific advances.