An Integrated Multifunctional Lab-on-a-Chip Platform for High Throughput Optical Mapping of DNA

Abstract

Direct Linear Analysis (DLA) technology employs continuous microfluidic elongational flow to stretch and optically map individual DNA molecules. Sequence specific tagging of DNA molecules with bisPNAs enables genomic differentiation between species. We report on the operation of a microfluidic lab-on-a-chip platform with the integrated functionality of sample concentration, fractionation, and high throughput optical mapping. Integration of the components on a single chip enables high throughput analysis of sub-nanogram samples. Previously described DLA devices [1] had throughput rates that were directly proportional to the initial sample concentration. Integrated on chip concentration in conjunction with tunable sample delivery flow rates to the DLA component allows for dynamic optimization of throughput to 12,000 kbp/s, independent of the initial sample concentration. In addition, fractionation of the sample enhances information throughput by discarding shorter fragments with lower information content prior to the optical mapping step. This integrated microfluidic device has been demonstrated in conjunction with a macrofluidic upstream sample preparation chamber in an automated system. This research was supported by the Department of Homeland Security Science and Technology Directorate. [1] Phillips et al, Nucleic Acids Research, 2005, 33 (18), 5828.