Ruthenium complex binding to DNA G-quadruplexes

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In 2013 it was shown for the first time that the DNA 'knot' known as the G-quadruplex was present in human cells. A single strand of DNA containing four runs of guanine bases with the sequence -GGG- in each, for example, can fold up in the presence of potassium ions to give a rather stable structure. For many years, this was a lab curiosity, of interest to nucleic acid enthusiasts but of little practical benefit. This situation changed strikingly once the structures were shown to be part of the intrinsic mechanism of the living cell. The best known structure is that found at the ends of chromosomes, which mainly consist of large amounts of double helical DNA. At one end, there is what looks like a frayed end, a single strand consisting of hundreds of repeats of the DNA sequence -GGGTTA-. In normal ageing these frayed ends become shorter and shorter as the cell repeatedly divides, leading to eventual cell death. More recently, though, it has been estimated that the human genome contains maybe 300,000 regions where a G-quadruplex could form. Importantly, some of these are now thought to be associated with the switching on and off of genes. Cancer and other diseases of the genes are associated with the inappropriate switching of genes, often as a result of genetic damage. Therefore there is great interest in small molecules which can interact specifically with these knots, to recognise them, to trap them, and to visualise them for example. Hundreds of such molecules are known, with varying degrees of specificity and binding strength.In Reading we have carried out 3D structural work on the binding to DNA of a group of ruthenium compounds related to the so-called 'light-switch' compound, which takes its nickname from is luminescence (glow-in-the-dark) property when bound to DNA but not in water. There is a large family of compounds with related properties, some causing DNA damage on irradiation and therefore of interest for possible tumour therapy. Our work has shown the structural origin of the luminescence and the DNA damage.In this work we will develop compounds showing specific recognition properties for G-quadruplexes. These compounds will not bind at all to normal double helical DNA but would just recognise the 'knot', and ideally, specific 'knots'. We have unpublished results which give us some strong pointers, including a crystal structure showing one of our new ruthenium complexes bound to a G-quadruplex. Our Japanese collaborators have other preliminary results strongly suggestive of specificity as well, using another of our new complexes. First, the copying process of normal DNA in living systems requires, among other things, the disentangling of these 'knots'. One of our compounds greatly hinders this knot-untying process, suggesting a strong and specific binding. Second, it is now possible to buy an antibody which binds specifically to the 'knots' in whole cells, but again, the binding mode of the antibody is not yet clear. This is a different way to study how the 'knots' are involved in cell regulation, and can be used to study healthy vs cancerous cells. This compound displaces the antibody, again suggesting strong and specific binding.