Innovations in DNA analysis device technology: Exploiting the effects of scale.

Abstract

This dissertation focuses on the development of novel systems for miniaturized DNA analysis. The design of these systems exploits the nature of fundamental phenomena such as conductive heat transfer and fluid mechanical instability on the length scales of interest to achieve devices with enhanced functionality compared with existing technology. We describe the design and operation of a multiple reaction system for parallel analysis operations that relies on steady-state temperature gradients through the device substrate to power multiple thermal reactions in parallel. Studies were performed on the scale-down of the Polymerase Chain Reaction (PCR), a ubiquitous technique for DNA amplification, in high surface-to-volume ratio microchannels. One possible application of these high surface-to-volume ratio microchannels is the counting of individual nucleic acid molecules through amplification. In addition, we studied and developed fluidic systems using a temperature gradient driven fluid mechanical instability phenomenon, Rayleigh-Benard convection. This natural convection phenomenon presents a faster, low-power and elegant alternative to conventional thermocycling for PCR. We describe the use of polymeric devices where the steady-state vertical temperature gradient through the material serves as the driving force for the convection that drives the process of DNA amplification. Geometric modifications such as closed-loop flows for fluid pumping and reactions, droplet mixing, and prospects for further miniaturization are also developed and discussed.