A Platform for Handheld Ultrafast PCR

Abstract

The Polymerase Chain Reaction (PCR) is one of the most sensitive and specific diagnostic tools available today. Yet, it stands out of reach for many vulnerable populations because commercial solutions are expensive, bulky, and require a steady electrical connection. The vast majority of designs that attempt to fill in this gap use Peltier elements for heating and cooling. In this work, I develop a mechanism that promises the same benefits, but without the drawbacks: optical heating. Peltier elements are easy to use, have no moving parts, and are widely available, but suffer from a critical flaw: energy inefficiency. This is because they cannot directly deliver heat to a 10μL drop of reagent: they need extra scaffolding, such as a thermal block, to conduct the heat. Optical heating can sidestep this by directly heating a tiny chamber that holds the drop, minimising wasted heat. Commercially available LEDs with 65% radiant efficiency, coupled with highly absorbing inks (>99% absorption) promise extremely high efficiencies with correspondingly long battery life, but in this dissertation I demonstrate that even generic high-power LEDs combined with black permanent marker from the local stationery store are efficient enough to do the job. The bulk of my work has focused on developing a framework for a device that can be realised with no moving parts, no optics, and cheap, widely available components, materials, and processes. With this apparatus, I demonstrate heating and cooling rates of 11 and 8°C/s respectively, permitting ultrafast PCR operation, bringing the time required for a full 35-cycle PCR (with a 3 min hot-start and 2 min final elongation) down from an hour to only 15 minutes. Fast thermal cycling is only a part of the task at hand. Ensuring that an ultrafast PCR diagnostic assay works with the device requires further tuning of the device and work with the chemistries. The final sections of this work outline a variety of paths forward, towards realising a working ultrafast PCR device, ultrafast qPCR, and increasing the throughput of the device to more than 1 sample at a time.