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Scientific Frontline: Extended "At a Glance" Summary: Synthetic DNA Gene-Targeting
The Core Concept: Scientists have developed a novel methodology to recognize and bind to a vastly expanded range of DNA sequences, including damaged DNA, by utilizing synthetic molecules. By incorporating artificial bases into triplex-forming oligonucleotides, researchers can accurately target specific genetic locations under normal physiological conditions.
Key Distinction/Mechanism: Historically, triplex-forming oligonucleotides operated like a restricted lock-and-key mechanism that recognized a narrow set of sequences and typically required acidic environments to function. The integration of an expanded genetic alphabet introduces new molecular key shapes, enabling these structures to bind selectively to a much broader spectrum of targets without requiring altered pH levels.
Major Frameworks/Components:
- Triplex-Forming Oligonucleotides (TFOs): Programmable synthetic DNA molecules designed to bind to specific locations within double-stranded DNA.
- Artificially Expanded Genetic Information System (AEGIS): A framework that extends the standard four-letter genetic alphabet to include synthetic bases, providing novel structural recognition capabilities.
- Oxidative DNA Lesions: Forms of cellular DNA damage produced by routine metabolic processes, which the engineered molecules are programmed to detect.
Branches of Science: Molecular Genetics, Bioengineering, Molecular Diagnostics, and Nanotechnology.
Future Application: This expanded recognition system provides a foundational platform for developing advanced tools in biotechnology and nanotechnology. Future applications include utilizing these programmable molecules inside cells to control gene activity and accurately target cancer-linked genes.
Why It Matters: The ability to reliably detect and bind to a diverse array of genetic targets breaks a decades-old bottleneck in molecular biology. This capability paves the way for highly precise, accessible diagnostic tools and targeted therapies for complex genetic diseases.
Researchers have developed a promising new approach that uses synthetic DNA molecules to target cancer-linked genes directly, opening new possibilities for future treatments, diagnostics, and biological research.
The study focuses on a long-standing challenge in genetic medicine: how to accurately target specific sections of DNA inside cells. While many modern genetic medicines work by targeting RNA, the molecule that carries genetic instructions from DNA, directly targeting DNA itself has proven much more difficult.
Dr. David Rusling, Associate Professor in Bioengineering from the University’s School of Medicine, Pharmacy and Biological Sciences, is the lead author of the paper and has worked in the field for more than 20 years. He said the new approach could provide a more precise way of controlling gene activity.
"Most drugs target proteins, which are the end product of a long biological process," Rusling said. "If you target DNA directly, you're working at the very start of that process. Each cell only contains two copies of a gene, so in theory, it offers a highly efficient way to influence how genes behave."
The team used specially designed pieces of synthetic DNA known as triplex-forming oligonucleotides, or TFOs. These molecules are designed to recognize and attach to specific DNA sequences, allowing researchers to target individual genes while leaving the rest of the genome untouched.
A major obstacle has been that naturally occurring DNA bases do not bind strongly enough to double-stranded DNA to be effective inside cells. To overcome this, the researchers incorporated a commercially available synthetic DNA base known as Z.
The modification allowed the synthetic DNA molecules to bind more strongly and selectively to difficult-to-target regions of DNA that contain high levels of the genetic building blocks guanine (G) and cytosine (C). These GC-rich regions play important roles in controlling gene activity but have historically been challenging to access.
The researchers tested the approach on MYC, a gene that is known to drive the growth of many cancers when it becomes overactive. The modified DNA molecules successfully attached to the target DNA and reduced MYC gene activity by between 50 and 80 percent in laboratory experiments.
Importantly, the new molecules outperformed both unmodified DNA and several previously developed approaches that attempt to target the same DNA regions.
"Triplex-forming oligonucleotides were a beautiful idea, but in many ways, biology defeated the original concept," Rusling added. "They could recognize DNA very precisely in a test tube, but the chemistry of natural DNA meant that many important sequences could not be targeted effectively under the conditions found inside cells. What we are doing is changing that chemistry rather than abandoning the idea."
The work also addresses a practical problem that has slowed progress in DNA-targeting therapies. Previously, many specialized DNA modifications had to be custom-made by expert chemists, making them difficult for other researchers to access. The modified bases used in this study are commercially available, making the technology much easier for laboratories around the world to adopt.
"What I really like about this chemistry is that if we can obtain these molecules, other researchers can too," Rusling said. "That accessibility means the whole field can move forward much more quickly."
Beyond its potential role in treating disease, the technology could become a valuable research tool. Scientists could use it to temporarily switch off individual genes and study how cells respond, helping improve understanding of everything from cancer biology to genetic disorders.
Because the system relies on DNA sequence recognition, researchers believe it may eventually be adapted to target many different genes simply by altering the sequence of the synthetic DNA molecule.
While further research will be needed before the technology could be used in patients, the study demonstrates a powerful new method for precisely targeting genes and regulating their activity.
Funding: D.R. and R.M. thank the Academy of Medical Sciences (BB/L021730/1) for funding support. S.A.B. and S.H. thank the National Institutes of Health (R01AI135146) and the U.S. National Science Foundation (MCB-1939086) for funding support.
Published in journal: Nucleic Acids Research
Authors: Ruolin Ma, Michael Brazzill, Dylan Justice, Nicholas Buckham, Cen Chen, Shuichi Hoshika, Steven A Benner, and David A Rusling
Source/Credit: University of Portsmouth
Edited by: Scientific Frontline
Reference Number: gen110326_01