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Quadruple Helix DNA Exists In Human Genome

60 years after Cambridge researchers Watson and Crick published their discovery of “double helix” DNA, the molecule of life, another team at the same UK university has published proof that four-stranded “quadruple helix” DNA also exists within the human genome. They hope their discovery will lead to a new generation of targeted cancer therapies that use synthetic molecules to trap the complex DNA structures and thereby stop cancer cells multiplying.

Lead investigator Shankar Balasubramanian, a professor at Cambridge University’s Department of Chemistry and Cambridge Research Institute, says in a statement:

“We are seeing links between trapping the quadruplexes with molecules and the ability to stop cells dividing, which is hugely exciting.”

“The quadruple helix DNA structure may well be the key to new ways of selectively inhibiting the proliferation of cancer cells. The confirmation of its existence in human cells is a real landmark,” he adds.

Balasubramanian and colleagues write about their findings in the 20 January online issue of Nature Chemistry.

From Concept to Test Tube to Living Cells

Their discovery marks the end of 10 years research to prove that four-stranded quadruple helix DNA structures, known as G-quadruplexes, also occur in living human cells.

They are called G-quadruplexes because they form in regions of DNA rich in Guanine, one of the four chemical bases or building blocks that encode genetic information (the other three are Adenine, Cytosine, and Thymine).

The team started with hypothetical computer models of the quadruplexes, then made synthetic versions in test tubes, and then proved, using fluorescent biomarkers, that the structures exist in real life in human cancer cells.

Although there is evidence that G-quadruplexes occur in single-celled organisms called ciliates, this is the first time they have been seen in human cells.

Links to Increased DNA Replication, Cancer Genes

In their paper, Balasubramanian and colleagues also show that the quadruplexes are more concentrated in genes of cells that are rapidly dividing, such as cancer cells.

Balasubramanian says this suggests targeting the quadruplexes could form the basis of new personalized treatments.

To detect the quadruplexes, lead author Giulia Biffi, a researcher in Balasubramaninan’s lab, made antibody proteins that bind to them.

The team were able to see “hot spots” in the genome where there were concentrations of four-stranded DNA because they tagged the antibodies with fluorescent markers.

While four-stranded DNA is spread fairly evenly through the genome of human cells and their division cycles, it appears they become more concentrated during the “s-phase” of the cell cycle. This is the point just before the cell divides, when the DNA replicates.

This discovery is an important step in cancer research because a key feature of oncogenes, a group of genes that drives cancer, is they have mutated in a way that increases DNA replication, which leads to uncontrolled cell proliferation and tumor growth.

The increased replication rate in oncogenes increases the concentration of the complex structures.

Targeting and Trapping Quadruplex DNA

The researchers found if they used an inhibitor to block DNA replication, quadruplex levels went down, showing DNA is dynamic, continually forming and unforming structures.

They experimented with targeting the quadruplex DNA:

“We have found that by trapping the quadruplex DNA with synthetic molecules we can sequester and stabilise them, providing important insights into how we might grind cell division to a halt,” says Balasubramanian.

Before that they had also discovered that an overactive gene with more quadruplex DNA is easier to interfere with. Perhaps this means it will be easier to trap the quadruplex DNA in certain cancer genes.

Although there is still a lot they don’t know, Balasubramanian and his team suspect that the quadruplex structures are like knots or tangles in the DNA during replication.

One question that the team is pondering is whether the complex structures have evolved for a reason.

“It’s a philosophical question as to whether they are there by design or not – but they exist and nature has to deal with them. Maybe by targeting them we are contributing to the disruption they cause,” asks Balasubramanian.

“Many current cancer treatments attack DNA, but it’s not clear what the rules are. We don’t even know where in the genome some of them react – it can be a scattergun approach,” explains Balasubramanian.

But he describes the fact it may now be possible to to target particular cancer cells that have genes with these features, and that they could be more vulnerable to such interference than normal cells, as a “thrilling prospect”.

The study was funded by Cancer Research UK, whose senior science information manager, Julie Sharp says:

“This research further highlights the potential for exploiting these unusual DNA structures to beat cancer – the next part of this pipeline is to figure out how to target them in tumour cells.”

Using a new online method, Cancer Research UK scientists recently identified 46 new potential druggable cancer genes from a list of 479.

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