A new dimension to DNA and personalised medicine of the future

G-quadruplex DNA Credit: Jean Paul Rodriguez

By investigating the existence of an unusual four-stranded structure of DNA in human cells, scientists have opened the door to novel cancer therapeutics and a new era for personalised medicine.

When Watson and Crick discovered the double helix structure of DNA in 1953, they declared they had "found the secret of life". However, as in all pursuits of science, the story did not end there. Less than 60 years later, a team led by chemist Professor Shankar Balasubramanian and cancer biologist Professor Steve Jackson has found that an unusual four-stranded configuration of DNA also forms at sites across the human genome in living cells.

Although known about by scientists for decades, the structure was considered to be something of a structural curiosity rather than a feature found in nature. It forms in regions of DNA that are rich in one of its building blocks, guanine (G), when a single strand of the double-stranded DNA loops out and doubles back on itself, forming a four-stranded ’handle’ in the genome.

G-quadruplexes have been known to occur at the ends of chromosomes in the regions known as telomeres, but it wasn’t until a strong association had been noticed with genes responsible for cell proliferation that Balasubramanian and others began to suspect that G-quadruplexes might be a potential target for cancer therapy. "If you synthesise a quadruplex-binding molecule and put it into cancer cells, it can impair the growth of these cells," he said. "We’ve come such a long way from thinking that we understand the genome - and it appeared that this structure could tell us something new."

Raphaël Rodriguez, a Senior Research Associate who has worked with Balasubramanian for the past seven years, developed a small synthetic drug called pyridostatin to target G-quadruplexes. Two years ago the pair joined forces with Jackson, whose lab is studying the fundamental biology of cancer. In a recent article published , they showed that not only do these structures form in cancer cells - the first time this has been demonstrated - but that pyridostatin can actually interact with G-quadruplexes to prevent proliferation of these cells. Although the function of G-quadruplexes remains a mystery, the discovery holds great potential for new, more selective approaches to treating cancer via interference with the genome, as well as offering a new dimension to personalised medicine.

Protecting the genetic code

At the heart of the new discovery is an innovative way of locating the structures in living cells and then ’capturing’ them for further examination. The scientists discovered that when pyridostatin binds to G-quadruplex DNA it causes a double-strand break in the double helix when the cell tries to replicate and copy its genes: "Pyridostatin binding to G-quadruplexes is a major impediment to copying the genome - so if a cell tries to replicate, this will generate breaks in the DNA," said Jackson.

Over the years, Jackson’s lab has found that there are certain proteins in the cell that act as molecular policemen, patrolling the nucleus of the cell looking for damaged DNA. If they detect damage, they start making repairs, and at the same time set off alarm signals to alert the rest of the cell that there’s a problem.

When there is no DNA damage, these molecular policemen are distributed evenly throughout each cell’s nucleus. But when cells are treated with pyridostatin, they congregate in specific locations on the DNA, indicating regions of damage, and showing up as dots under the microscope. "The field really jumped on the idea that these dots represent telomeres that have G-rich sequences and in vitro have the potential to form G-quadruplexes," said Jackson. "But we stained the dots for telomere proteins and found there was only a small amount of overlap. So clearly, this pyridostatin compound is inducing DNA damage in lots of other places, and we were faced with the issue: ’if they are not telomeres, what are they?’"

This confirmed an earlier finding in Balasubramanian’s lab by Julian Huppert, then a PhD student, who devised a computational search algorithm to map out every spot in the entire human genome that had potential to fold into a G-quadruplex. He found there were close to 350,000 of them.