Microfluidic large scale integration and its application to systems biology

Abstract

The goal of biology is to understand how complex systems such as cells and entire organisms function. Systems Biology attempts to quantitatively characterize all components comprising these systems. A considerable task. Microfluidics provides a powerful tool for undertaking this endeavor. This thesis describes the development of Microfluidic Large Scale Integration (MLSI) using devices fabricated by Multilayer Soft Lithography (MSL). MLSI and fluidic components, such as multiplexers and free-standing membranes, serve as the infrastructure for performing large-scale biophysical measurements of biological systems. Transcription factor binding energy landscapes were determined using MLSI and MITOMI, a novel method for measuring molecular interactions. The biophysical characterization of transcription factors described herein were the first comprehensive measurements of its kind, and answered basic questions regarding how transcription factors recognize DNA. Furthermore, it was possible to predict the in vivo function of transcription factors using only the measured binding topographies and a genome sequence, indicating that biological processes can be predicted with high accuracy. More generally, the methods described in this thesis are generally applicable to understanding the properties of any biological system and should find broad usage in the field of Systems Biology.