Single molecule DNA sequencing in gold.

The human genome contains 3164.7 million nucleic acid bases (adenine, guanine, cytosine, thymine) and it is estimated that the length of all the DNA strands in a single cell (if all the strands were placed end to end) is about two metres. The human genome sequence was completed at the start of the millennium; this resulted in significant public and scientific interest in understanding the DNA sequence 'code' and how it is 'translated'. The sequence of the genome provides information about our ancestry, hereditary diseases, our features (such as eye, skin or hair colour) and our physiological 'make-up'. In order to truly understand the genome sequence it would be desirable to have simpler DNA sequencing methods so that many more genomes could be sequenced. Currently, methods require expensive reagents, are laborious and take a long time. Despite the fact that the human genome was sequenced a decade ago and better DNA sequencing methods have been since developed, a simple, cheap, fast, accurate DNA sequencing method is still an important goal. In our view, what is needed is a small scale technology, something that works like a hard disk drive, where a tiny read head is scanned past the stored information (the DNA strand) and the information (the sequence) is read directly without need for any complex processing of the genomic DNA molecule. We propose to flow DNA molecules through a nanopore that will act as a 'read head' and detect and identify the nucleic acids in the DNA sequence by their response to laser excitation. Identifying the DNA base sequence in this way will be highly ac curate, and capable of detecting damage or modification to particular bases from environmental or cellular processes which can control the switching on and off of genes. DNA sequencing techniques are crucial to obtain a better understand of all organisms, not just humans, and a fast, cheap DNA sequencing method will be able to answer many more questions as well as also provide a diagnostic tool. These studies will provide proof of concept data appropriate to demonstrate a very new DNA sequencing approach.

A one year proof of concept study is proposed to demonstrate a new method for single molecule DNA sequencing that allows for the direct spectral identification of the nucleic acid bases in the sequence. This approach should ultimately allow for fast, accurate sequencing without the need for enzymes such as polymerase. Nanostructures will be fabricated and DNA molecules will be transported in fluid through the structures. An optical set-up will be built that allows for the direct detection of DNA nucleic acid bases in a sequence dependent manner. This study will build upon our expertise in DNA chemistry, bioanalytical devices and near-field optical approaches.

The UK has a significant and growing commercial activity in the field of diagnostics and DNA sequencing technologies. A methodology that provides improvements over existing DNA sequencing methods has a clear commercial potential. It is important to be realistic - a one year 'proof of concept' study is proposed and this is not going to reach a technology readiness level that is anywhere close to a product that could be commercialised or that could be of interest to venture capitalists. Even so, we have had informal discussions with Renishaw Diagnostics, who have shown a strong interest and we plan to cement a more solid collaboration in the longer-term with them. In addition members within the collaborative team have (i) a track-record for commercialising their research through start-up companies and (ii) current collaborative activities with members of commercial companies involved in DNA analysis and sequencing technology (as outlined in our 'Pathways to Impact' document). Nanoporous technologies, of the type proposed, might also be useful for the detection other small biomolecules such as metabolic products (in body fluids), pharmaceutical agents and environmental pollutants. In order to achieve the impact of our research we will engage with members of the environmental and pharmaceutical, industrial, public or private sectors, once our results are protected. The realistic timescales for the benefits to be achieved will be beyond that the 'proof of concept' study proposed here. The research is clearly 'high risk/high reward' and very adventurous (thus fitting the 'Early concept, exploratory investigations of new tools, technologies and resources' within the current call). We envisage that a further 3 year period of study is required to demonstrate the methodology for 'real' DNA sequencing in a robust and reliable manner. The impact of achieving this would be substantial.