Andrew J. Bonham

Research Abstract

Our ability to analyze, understand and practically benefit from the control logic encoded in the human genome is currently limited by a lack of accurate information regarding promoter regulation. Gene regulatory proteins play critical roles in converting the genome into the complex ensemble of expressed genes. In this project, we are working to develop an optical, reagent-free approach relying on nanoparticle/DNA assemblies to identify DNA sequences bound by individual proteins and protein assemblies. This will provide a new analytical tool for the rapid identification of DNA sequence preferences for individual proteins which regulate gene transcription; further, this approach provides a basis for investigating complexes of such proteins and simultaneously determining how such complexes differentially assemble onto different genetic elements. Currently available complementary technologies are complex and limited to the antibody-based detection of DNA segments bound by a single type of protein. Our approach is based on a highly sensitive optical method, surface enhanced Raman spectroscopy (SERS), and offers multiple methodologies of detection. Preliminary results show the detection of protein binding to several types of nanoparticle/DNA assembly. Current work is focusing on additional well known sequence-specific DNA binding proteins, with subsequent applications where gene chip arrayed nanoparticle/DNA assemblies will be used to interrogate well characterized cells, such as yeast. The ultimate goal of the proposed research is to develop a SERS-based protein binding microarray (SERS-PBM) technology for the rapid identification of DNA binding affinities and preferences for proteins and protein complexes involved in genetic regulation.