Ruthenium complex binding to DNA G-quadruplexes

Lead Research Organisation: University of Reading
Department Name: Chemistry

Abstract

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 We have unpublished results which give us some strong pointers, including a crystal structure showing one of our new ruthenium complexes bound to a G-quadruplex.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.

Technical Summary

Photoactive ruthenium polypyridyl complexes are versatile and tunable for a range of applications in the life sciences because of their interactions with nucleic acids. The photoactivity can be harnessed as a diagnostic 'light switch' or towards DNA damage. In Reading we have become world leaders in understanding these interactions using a combination of a range of spectroscopic techniques combined with X-ray crystallography. Recently we examined the specific question of synthesising new complexes with high G-quadruplex/duplex preference, making use of our existing structural information. This is a very active field since the demonstration that G-quadruplexes can be recognised by specific antibodies in living cells, and furthermore, that G-quadruplex forming sequences play a key role in promoter regions of the human genome. The interaction of G-quadruplexes and our ruthenium complexes is determined by the rigidity and inertness to substitution of the complexes, and as we have recently shown, by the substituents on the dppz ligand. We have defined a structural basis for the clear lambda enantiomer preference and now seek to define the role of the extended dppz chromophore in the G-quadruplex interaction. We will carry out a range of synthetic studies to optimise further our ligand design, aiming to optimise both the binding constant and the luminescence properties. The photooxidising TAP complexes are useful tools, since quenching of the luminescence indicates binding adjacent to a G-quadruplex, whereas binding to loop regions containing only adenine and thymine residues gives enhancement of luminescence. We already have some X-ray data showing enantiomeric binding to loops in the human telomeric quadruplex and aim to develop full high resolution structural models. With our partners we will study the inhibition of G-quadruplex replication by these complexes and the effect on the binding of the BG4 antibody in a range of cell lines.

Planned Impact

The fundamental nature of the proposed research has clear benefits to the academic community, with insights into the binding of enantiomers of ruthenium complexes to G-quadruplexes. Behind this academic impact is a range of scientific techniques that require a high level of skill and coordination from the interdisciplinary team to optimise the techniques and to develop a coherent interpretation of the results. The PDRA and technician will enhance their skills within a variety of techniques, and be able to use these skills in subsequent employment. Several members of the Cardin group who have developed key skills in crystallography as students and PDRAs within the group have gone on to obtain positions at central facilities such as Diamond Light Source, ILL and NPL, as well as industries such as GSK and Evotek. Several of the technicians have gone on to BSc or MSc level studies in chemistry, environmental chemistry and pharmacy, or to more senior analytical roles, and one is in permanent employment in Diamond Light Source as a Laboratory Instrument Technician.
The detection and specific targeting of nucleic acid assemblies such as the G-quadruplex is relevant to the design of new fluorophores and therapeutically active species. Ruthenium complexes have been considered promising candidates for photodynamic therapy for several years. The proposed research will enhance our understanding of the complex nature behind DNA binding, especially of the different enantiomers and extended chromophores. If pharmaceutical companies are to develop these metal complexes into drugs for treatment of disease, then a full understanding of selective or specific binding is essential, along with knowledge of how derivatisation can tune the binding properties.
The awareness of the public about DNA structure is often limited to that found in biology textbooks, most commonly the double helical nature of DNA. Some may be aware of the damage that chemicals can do to human health, but the underlying mechanisms and structural changes to DNA that occur are not as well known. The team in Reading have an expertise in understanding and visualising the structure of DNA and putting these structures into a biological context. Using our expertise to show how DNA can adopt multiple structures, and that these structures can be damaged to different degrees and in different ways, will help to educate school-age students and the scientifically interested lay public to the importance of understanding how damage can occur and why it is important to protect our DNA from this damage, for example by wearing suntan lotion, or refraining from smoking. As a part of this project, an extensive programme of outreach activities will be undertaken (as detailed in the Pathways to Impact), the aim of which is to educate students and those interested in science about our work and how nucleic acids are relevant in everyday life.
 
Description Kobe_FIBER collaboration 
Organisation Konan University
Country Japan 
Sector Academic/University 
PI Contribution Setting up crystallisations of nucleic acid-ligand complexes of interest to the team in Kobe.
Collaborator Contribution (when it will be possible) biological testing of new compounds prepared in Reading.
Impact It has not yet been possible to take advantage of this collaboration as it applies to this grant, due to covid-19 restrictions on travel.
Start Year 2019