Towards high efficiency microfluidic DNA extension for genomic analysis

Abstract

Genomic analysis and DNA sequencing is a mature field with many established techniques. Developments in micro- and nanofabrication over the last decade or more have brought advances in a number of areas of chemical and biological analysis and genomics has been of particular interest. This thesis presents the development of two new techniques in microfluidic DNA manipulation that are directly applicable to the fabrication of next-generation genomic analysis devices.

A key area for any miniaturised device is the ‘world-to-chip’ connection. Even the most highly integrated micro total analysis systems require efficient sample loading and for sensitive detection as well as device reuse it is essential that molecules of interest are not lost in the world to chip transition. A new type of microfluidic interconnect is described in this work, which uses a shallow slope to make an inplane connection between a microfluidic channel and a glass capillary. The microfluidic channel is fabricated in silicon capped with glass. The phenomenon of deep reactive-ion etch (DRIE) lag was applied to fabricate the slope and DRIE was also used to fabricate the microfluidic channels. The interconnect has been demonstrated to provide low loss loading of 48.5kbp DNA molecules from world to chip and is fabricated using standard silicon processing equipment.

The second new development reported in this thesis is the design, fabrication and characterisation of microfluidic DNA ‘preconditioning’ channels which are used to improve the efficiency of a downstream taper in the channel used for fluidic DNA extension. Extension of DNA in elongational flow has the potential to become a high-throughput genomic mapping technology. A common limitation to all systems previously demonstrated for stretching DNA with an elongational flow is that the stretching efficacy is strongly dependent upon the initial conformation of the DNA strand. The devices described in this thesis demonstrate an improvement in DNA preconditioning using non-contact microfluidic shearing flow in order to deliver extended molecules to a microfluidic channel in which optical interrogation of fluorescent markers takes place using a bespoke confocal spectroscopy system.

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