The aim of this project is to use solid-state nanopores to recognize and characterize transcriptional regulatory proteins (transcription factors or TFs) bound to genomic DNA. Nanopores have been extensively used to characterize DNA translocation, DNA and RNA unzipping, and DNA-enzyme interactions, at the single molecule level. These methods will be extended to map the interactions of regulatory proteins with DNA, and to study questions that are not easily addressable by classical methods. Focused research will be conducted to establish the relationships between the proteins' size, shape, charge and other properties and the ion blockade signal in the nanopore translocation experiments. A team of a biophysicist (PI: Meller, nanopore physics) and a biomedical engineer (co-PI: Weng, gene regulation) will conduct extensive characterizations of proteins under different conditions such as pH, ionic strength and temperature to generate an electronic table, which uniquely relates each regulatory protein (or regulatory protein family) with a set of experimental observables. This study will be complemented with a broad bioinformatics analysis of the same protein in its capacity as a transcription factor. The effects of cooperative and competitive protein binding in biological systems will be also addressed.
These studies are directly related to gene expression and regulation, and therefore have broad implications in basic sciences as well as in gene therapy and drug discovery. On the educational side, nanopore physics and its applications to gene regulation will be introduced in lectures in Biological Physics and Bioinformatics as advanced topics, providing opportunities for students in biophysics, molecular biology, and applied physics to explore state of the art research outsides the classical boundaries of their disciplines. The work will also engage summer students through the Boston University NSF funded REU program and will engage inner-city high school students in this interdisciplinary cutting-edge research, by developing project-based, hands-on activities for the summertime residential Upward Bound program (85 students per year from near poverty-level households). This program will significantly enhance the science education and opportunities for first time college-bound high school students.
