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Nanofluidic Methods for Mapping Epigenetic and Genomic Variation

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DNA stretched to the limit for photo ID

Methicillin-resistant Staphylococcus aureus (MRSA) bacteria are a serious threat to many patients, particularly in hospitals. Rapid detection procedures for identification of MRSA are essential to allot special care to such cases.


The DNAMAP (Nanofluidic methods for mapping epigenetic and genomic variation) project focused on optical mapping of stained, denatured DNA. Developed recently, this MRSA detection procedure involves introducing the DNA into a nanofluidic system. Subsequent manipulation and imaging gives a map, which is then compared with an existing reference genome. Project work investigated how to use micro- and nanofluidic systems for the mapping procedure. When the system is further automated, detection of MRSA strains will be speeded up and cost of the procedure potentially reduced. Researchers investigated the effects of nanochannel dimension. The team used 150nm wide and high nanochannels initially for DNA analysis. However, when reduced to 50nm, the DNA is stretched to 85 % its original length as opposed to 50 %, thereby improving imaging and resolution of the DNA. Furthermore, insertion of smart inlet structures aided DNA to pass from a microchannel – where it was coiled – to a nanochannel in which it is stretched. Application of electric potentials across the nanochannels speeded up the movement of the DNA. New approaches to micro- and nano-fabrication were explored including characterisation, focusing mainly on scanning electron microscopy. Improved systems for provision of a cleanroom involved device planning and process design. Researchers also worked on dry and wet etching techniques, electron-beam lithography, and device bonding. A teaching programme integral to DNAMAP dealt with all fabrication processes. The course also dealt with problems the project encountered including an issue with entanglement of the DNA isolated from single cells. DNAMAP has constructed a substantial knowledge platform on the improvement of detection methods for MRSA. Application of the research results can be extended to many other procedures involving the identification of particular DNA.


DNA, MRSA, identification, nanofluidic system, imaging

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