Synthetic DNA toolkit expands scientists' ability to recognise genetic targets

A new method for recognising and targeting DNA that dramatically expands the range of genetic sequences scientists can identify, has been developed by experts at the University of Portsmouth.  

Published this week in Nature Communications, the research opens new possibilities for gene-targeting technologies, molecular diagnostics and DNA nanotechnology. 

Dr David Rusling, Associate Professor in Bioengineering from the University of Portsmouth’s School of Medicine, Pharmacy and Biomedical Sciences, said: "Our lab develops synthetic molecules that can recognise and bind to unique gene sequences. By introducing synthetic DNA bases into these molecules, we've been able to significantly improve how they recognise their targets. 

"I've worked in this area for around 20 years, and this is the first time we've had a system that combines strong recognition under physiological conditions with building blocks that are commercially available to other researchers." 

The study overcomes longstanding limitations in a class of synthetic DNA molecules known as triplex-forming oligonucleotides (TFOs), which can be programmed to bind to specific locations within double-stranded DNA.  

Although TFOs have attracted interest as potential tools for controlling gene activity and detecting genetic changes, their usefulness has been restricted because they can recognise only a limited range of DNA sequences and typically require acidic conditions to work effectively. 

Dr Rusling said: “This work expands the range of DNA sequences that can be recognised using TFOs. By broadening the molecular recognition code and enabling strong binding under biologically relevant conditions, we have created a platform that other researchers can use to develop new tools for biotechnology and medicine.” 

The research team incorporated synthetic DNA bases from an Artificially Expanded Genetic Information System (AEGIS) first developed by the Benner laboratory in the US, a technology that extends the natural genetic alphabet beyond the four familiar DNA letters A, T, C and G.  

By systematically testing 120 different recognition combinations, the scientists identified a set of interchangeable molecular building blocks that enable TFOs to bind strongly and selectively to a much broader range of DNA targets under physiological conditions. 

“A useful way to think about it is that traditional TFOs were like a lock-and-key system with only a few key shapes available. This research creates many new key shapes, allowing scientists to unlock and recognise a much wider range of DNA targets,” added Dr Rusling.  

The researchers showed that the expanded recognition system can identify not only standard DNA sequences but also damaged DNA. In particular, the study demonstrated recognition of oxidative DNA lesions, a common form of damage produced by normal cellular processes.  

"Cells constantly experience DNA damage," said Dr Rusling. "What is exciting is that these new molecules can be designed to recognise some of those damaged sites as well as normal DNA sequences." 

The team is currently investigating the gene-targeting capabilities of the molecules inside cells and exploring applications in medicine, diagnostics, biotechnology and nanotechnology. 

The paper Recognition of non-standard base pairs by triplex-forming oligonucleotides containing an expanded genetic alphabet is published in Nature Communications.