The two helical chains of deoxyribonucleic acid (DNA) is an iconic symbol in science, but researchers recently unfolded the details into the three-dimensional structure of supercoiled DNA, a much more dynamic shape than the popular double helix and a likely ally in designing better medicines.
Reporting in the journal Nature Communications, researchers from the Baylor College of Medicine imaged different DNA shapes using a microscopy technique and examined them using supercomputer simulations at the University of Leeds.
The simulations revealed that the molecule of life is more than the rigid, static double helix structure highlighted by James Watson and Francis Crick in their celebrated 1953 paper.
An improved understanding of the appearance of the DNA – shown in research to have a dynamic, constantly wiggling and morphing nature – is believed to help scientists in producing new antibiotics, more effective chemotherapies and better drugs.
“[T]he action of drug molecules relies on them recognizing a specific molecular shape – much like a key fits a particular lock,” explained Sarah Harris, lead computer simulation researcher from University of Leeds’ School of Physics and Astronomy.
Harris argues that the shape of DNA is not always as simple as the double helix as when the duo described it decades ago, as they were focused on “a tiny part of a real genome, only about one turn of the double helix.”
According to Harris, their own research views DNA on a “somewhat grander scale” or at a couple of hundred of base pairs.
In humans, there are around 3 billion base pairs making up the complete set of DNA instructions, forming about a meter of DNA. The team replicated the coiling of DNA to study its structure when crammed into cells.
“A zoo of beautiful and unexpected shapes,” said co-lead author Rossitza Irobalieva when they coiled the tiny DNA circles through a potent microscopy method called cryo-electron tomography. The technique yielded the first three-dimensional captures of individual circular DNA molecules.
Experts at the University of Leeds then used a supercomputer for simulating the movement and shapes of molecules.
In an email interview, Harris underscored the potential of the research to improve medications’ molecular design as they are being created.
“[S]ome anti-cancer therapies bind to the DNA itself, and some antibiotics target the enzymes that specifically recognize supercoiled DNA in bacteria,” she explained.
Harris added that supercomputers will be increasingly involved in drug design while scientists will continue to do a “puzzle with millions of pieces” and changing shapes.
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