Design of a microfabricated device for ligase detection reaction (LDR)

Abstract

The objective was to design and manufacture a microscale Ligase Detection Reaction (LDR) device for detection of cancer-associated rare gene mutations. The LDR module will be incorporated with other devices such as a Continuous Flow Polymerase Chain Reaction (CFRCR) unit and a Capillary Electrophoresis (CE) chip in a modular lab-on-a-chip technology. During LDR, devloped by Francis Barany, several primers are mixed with the analyte, exposed to a thermal cycle consisting of two steps of 95°C and 65°C for 20 cycles, and cooled to 0°C. The first step in the design was to determine if the baseline time for the LDR reaction could be reduced from the 2½ hours required for the orignal reaction. Experiments have shown that it is posssible to obtain useable product from the LDR after 40 minutes, a 75% reduction, before going to the microscale, which should allow further improvements. Due to the extensive mixing needed prior to the reaction a set of alternative diffusion mixers was identified and microfabricated to determine which geometry was the most effective. Simulations of the thermal response of the device were done using finite element analysis (FEA) to compare to experimental results. The required temperature profile will be obtained by using resistive heaters and thermoelectric modules. A prototype LDR device was laid out based on the results of the studies.