Nanobaths for DNA analysis

Lead Research Organisation: University of Southampton
Department Name: Optoelectronics Research Centre

Abstract

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'. Despite the fact that the human genome was sequenced a decade ago and better DNA sequencing methods have been since developed, simpler, cheaper, faster DNA sequence analysis methods which do not necessarily provide the full genome sequence but detect specific differences in the sequence is an important goal. Thus to obtain information that is required without evaluating the whole sequence - essentially just like checking the key quotes from a Shakespeare play without reading the whole book 'cover to cover'.

In our view, what is needed is a small scale technology, something that works like a thermal reader, where a tiny read head is scanned past the stored information (the DNA strand) and the information (the differences in the sequence) is read directly without need for any complex processing of the genomic DNA molecule. We propose to flow DNA molecules through a nanocapillary with a light activated heater that will act as a 'read head' and detect and identify variations in the DNA sequence. The DNA is confined in channels meaning that the long DNA strand which can be microns long does not travel through all 'noted up'. Identifying variations in the DNA base sequence in this way will be very simple and fast, and we believe capable of detecting modifications to particular bases - notably sequence variations inherited from parents, from damage leading to cancers, from environmental or cellular processes which can control the switching on and off of genes. These sorts of techniques are crucial to obtain a better understand of the genetics of all organisms, not just humans, and a fast, cheap DNA analysis method will be able to answer many more questions as well as also provide a simple fast diagnostic tool. These studies will provide proof of concept data appropriate to demonstrate the potential of nanocapillaries for the first time for integration with optical approaches for single molecule interrogation in confined spaces. We believe these capillaries could be developed to provide simpler easier tools for other diagnostic applications.

Technical Summary

A 15 month proof of concept study is proposed to demonstrate a nanoscale technology for interrogation of single biomolecules. In the first instance a demonstration will be made to evaluate single molecule DNA sequence information. This is a relatively high risk venture, but we believe it vital to demonstrate nanocapillaries for the first time in this manner. This approach should ultimately allow for fast DNA analysis, for the evaluation of polymorphisms or DNA modifications in genomic DNA. Nanocapillaries will be fabricated, structures to provide localised nanoscale heating of the capillaries will be designed and integrate and then DNA molecules will be transported in fluid through the nano-capillary. Specific sequences will be detected by thermal melting and optical detection strategies. These proof of concept studies will allow us to bring together our optical fibre, DNA analysis, nanofabrication and applied theoretical approaches in order to deliver a technology that will ultimately provide a platform for simple interrogation of single molecules in solution in confined spaces.

Planned Impact

Nanocapillary technologies, of the type proposed, are anticipated to be of value for a much broader range of screening applications. 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 requirement of 'Early concept, exploratory research project application' within the current call). We envisage that a further 3 year period of study is required to demonstrate the methodology for 'real' DNA analysis in a robust and reliable manner. However with a demonstration of the integration of one nanoscale optical technology within the nanocapillaries for a bioanalysis application would provide the confidence for us to develop further the nanocapillaries with further integrated structures for the sensitive evaluation of single biomolecules. The impact of achieving our goals would be substantial.

Publications

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Description The use of glass capillaries with nanometer internal diameters have been demonstrated for the first time for nanofluidic applications and some fundamental science studies have been performed that we aim to exploit to understand the unusual filling processes shortly through developing theoretical models in the remaining period of the funding.
We are developing nanofibres for sensitive detection of DNA sequences, these have been created through tapering.
Exploitation Route We diverted our attention to the tapered optical fibres with respect to biosensing and with the input of a PhD student have demonstrated these on a model system for DNA sequence analysis; this used much of the technology developed during the short TDI funding. The use of this approach is being developed for the wavelengths used for optical communications as this technology is well developed for high frequency sensing applications.
Sectors Chemicals,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Cafe Scientifique 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Cafe Scientifique at the Isle of Wright. There are significant problems for residents on the island to get any sort of opportunity to attend any sort of public dissemination activity associated with science. It has always been disappointing to me that the educational results on the island are lower than on the mainland of Hampshire. A trip to the Isle of Wright from my department in the University is challenging and required approximately 3 hrs of travel one-way. Thus although this was a time-consuming activity the audience was especially enthusiastic. It was clear that the organisers struggled to attract speakers. The presentation that I delivered was appropriate to an audience with a very limited knowledge of genetics (and epigenetics) and the application of sequencing for stratified medicine. This resulted in a discussion of 1.5 hrs and only stopped because it was necessary to get a boat back to Southampton.
Year(s) Of Engagement Activity 2017