Professor Tom Brown Research Pages

Summary of Research

My research is interdisciplinary, focusing on nucleic acid chemistry and its applications in other fields including DNA diagnostics, forensic science and nanotechnology. In the early part of my academic career I used NMR and X-ray crystallography to study the properties of base pair mismatches in DNA and their implications for DNA repair. Examples of this research are the elucidation of the structures of DNA duplexes containing G.T (Nature 1985, 315, 604) and A.C mispairs (Nature 1986, 320, 552). This approach led us to determine the molecular basis of the mutagenic effect of a number of chemical lesions in DNA, for example O6-methyl guanine (Proc. Natl. Acad. Sci. USA 1990, 87, 9573). This was the first time that the structural basis of a mutation caused by chemical damage to DNA had been defined at the molecular level. Our studies also highlighted the fact that mispaired bases form distinct structures and cause minimal distortion to the overall conformation of the DNA duplex. Therefore enzymatic recognition of modified base pairs in living systems must depend upon subtle differences. To confirm this we investigated the origin of the recognition of mismatched and mutagenic bases by DNA repair enzymes. An example of this is our collaboration with Laurence Pearl to elucidate the structural basis of specific base-excision repair by uracil-DNA glycosylase (UDGase) and MUG (Nature 1995, 373, 487, and Nature Structural Biology 1998, 5, 697). These essential enzymes reverse the damage that is caused to DNA by oxidation of cytosine bases, recognizing the absence of a single methyl group to initiate excision-repair. UDGase is of interest as a target for antiviral therapy.

The expertise that we gained from these fundamental studies on DNA base pairing was then used in the emerging field of molecular genetics to develop new methods of mutation analysis.  In collaboration with AstraZeneca we invented a novel fluorescence-based real-time PCR method for the identification of mutations and single nucleotide polymorphisms (SNPs) in the human genome. This was one of the first successful technologies for rapid mutation detection and was patented, published in Nature Biotechnology (1999, 17, 804) and marketed as “Scorpion Primers” by a spin-out from AstraZeneca (DxS Genotyping Ltd). I am also co-inventor of “HyBeacons”, novel fluorogenic probes that utilises DNA melting temperature as a means of identifying mutations. HyBeacons, the result of a collaboration with the Laboratory of the Government Chemist, have recently been licensed to an International Biotech company. They can be used for the rapid diagnosis of bacterial infections and genetically-related diseases, and are also being developed by us for Forensic applications (New Scientist Jan 14th 2006). We recently demonstrated that such methodology has potential for rapid human identification at crime scenes and in custody suites, with clear implications for crime detection and related applications (Forensic Sci. Int. Genetics. 2008, 2, 333, Org. Biomol. Chem. 2008, 6, 4553). Our work on genetic and biophysical analysis of DNA is based on the synthesis of novel fluorescent oligonucleotides, a field in which we have a strong background (e.g. Nature Protocols 2008, 2, 615-623, and Nucleic Acids Res., 2002, 30, e39). In the field of DNA sequence analysis a collaboration with Philip Bartlett in Southampton recently led to a new method for identifying mutations in the human genome by a novel combination of SERS detection and electrochemical DNA melting (J. Am. Chem. Soc. 2008, 130, 15589). My work combines fundamental studies with applications, and have always had a strong interest in taking ideas from the research laboratory and turning them into useful tools for other scientists. I was the Founder of Oswel Research Products, the first UK supplier of high quality oligonucleotides and analogues which provided an essential service to chemists and biologists for many years. In Oswel we were able to synthesise oligonucleotide analogues that were not available from any other supplier. We had a long-standing relationship with the UK Forensic Science Service in their work on the National DNA database. Recently I have co-founded two other start-ups, ATDBio (on the Oswel model) and Primer Design. I also consult for several Biotechnology companies.

I am interested in the use of modified oligonucleotides as potential therapeutic agents and in this context we are trying to develop methods of reversing the mutations that give rise to genetic diseases. The basic idea is to initiate DNA repair by the formation of triple helices at the site of the mutation. Triplex forming oligonucleotides (TFO’s) have wider applications in molecular genetics, diagnostics, therapeutics and nanotechnology and for this work we have developed a set of four base analogues that, when incorporated into TFOs, are able to recognize mixed sequence DNA with high specificity. This was the first example of full sequence recognition of a DNA in the major groove (Nucleic Acids Res. 2005, 33, 3025). This work is a collaboration with Keith Fox in Biological Sciences in Southampton. My research has very recently moved in a new direction. We are using the copper-catalysed alkyne-azide coupling reaction to synthesise large covalently closed cyclic DNA structures (DNA catenanes) for use in biological applications and as scaffolds in nanotechnology. Our first paper in this field was one of the most cited JACS papers in 2007 (J. Amer. Chem. Soc. 129, 6859), and two other publications (ChemBioChem 2008, 9, 50, ChemBioChem 2008, 9, 1280) were amongst the most accessed papers when they appeared on the ChemBioChem web site. A recent collaboration with Bengt Norden’s group in Gothenburg involved this DNA click chemistry to elucidate the binding mechanism of a novel threading DNA intercalator (J. Am. Chem. Soc. 2008, 130, 14651). We have developed this chemistry further to synthesise DNA templates containing modified backbones which can be copied by polymerases during PCR. This discovery (J. Am. Chem. Soc. in press.) promises to open up a new field. With careful design it might be possible to use such methodology to synthesise functional DNA strands greater than 1000 bases in length entirely by chemical methods, an order of magnitude longer than is currently achievable. If the aim of this research is achieved it will be an important contribution to the new discipline of Synthetic Biology. A further collaboration with the Norden group led to the synthesis of addressable high-information-density DNA nanostructures (Chem. Phys. Lett. 2007, 440, 125). These constructs constitute scaffolds on which molecules can be attached at pre-determined locations with nanometre precision so that they can communicate in a controlled manner by energy or electron transfer.

My research spans several fields and a high proportion of my publications appear in biology, biochemistry and nanotechnology journals. Our endeavours have given rise to numerous new analytical techniques that are now used in the real world, particularly in the field of genomics and diagnostics. I have received recognition intenationally, for example I was one of the selected speakers at a Nobel Workshop addressing the frontiers of proteins and nucleic acids, another speaker being Andy Fire who was awarded the Nobel Prize for his discovery of RNAi, and in 2008 I gave a plenary talk, together with the Chemistry Nobel Laureates Barry Sharpless, Ryoji Noyori and Richard Schrock, at the Molecular Frontiers Symposium in Singapore.

January 29th 2009