Researchers have developed a synthetic molecule that can recognize and bind to double-stranded DNA or RNA under normal physiological conditions. The molecule could have broad applications for research purposes and for diagnosing and treating genetic disease. The molecule was developed as part of an international effort, including Carnegie Mellon University researchers, and the findings were published in Communications Chemistry.
The concept of designing a molecule to bind to and control DNA and RNA is not new, but the strong bonds between base pairs makes it challenging to get molecules into the double helix. The Carnegie Mellon University research team had previously designed and developed gamma peptide nucleic acids (gamma PNAs)—synthetic analogs to DNA and RNA that can be programmed to bind to genetic material that causes disease, allowing them to search for detrimental sequences then prevent them from malfunctioning.
The group also created double-faced gamma PNAs called Janus gamma PNAs that are able to recognize and bind with both strands of a DNA or RNA molecule. However, advancement of Janus gamma PNAs had previously been held back by two obstacles. The first was that only a small number of Janus bases could be made and these varied in shape and size. This meant the bases could only recognize repeats of the same set of base pairs and couldn’t recognize more complex sequences.
The second issue was that it was difficult to synthesize Janus bases for canonical base pairs due to the molecules binding to each other, preventing them from incorporating into DNA and RNA.
To overcome these challenges, the team created a new set of bifacial nucleic acid recognition elements to account for every possible combination of nucleobases that can be found in the genetic code, thus allowing recognition of complex genetic sequences. They also devised a novel solution and solid-phase synthetic method to develop the Janus gamma PNAs to prevent self-complimentary bases from hybridizing to one another.
With the new Janus gamma PNAs, the molecules were able to invade a canonical base-paired DNA or RNA double helix at a physiologically relevant strength and temperature. They do so by inserting themselves between base pairs during the fraction of a second when DNA and RNA molecules open for a fraction of a second to “breathe”.
The Janus gamma PNAs have potential uses in targeting DNA for gene editing and transcriptional regulation. They may also be used to alter the secondary and tertiary structures of RNA, which could someday lead to treatments for a number of neuromuscular and neurodegenerative disorders.
Image: Developed by researchers at Carnegie Mellon University, this janus gamma peptide nucleic acid (PNA) can invade the double helix of DNA and RNA. Image courtesy of Carnegie Mellon University.