Andrew J. Bonham
Visit Andrew's Online ProfileResearch 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 my projects, I am working to develop novel spectroscopic approaches to identify and characterize the binding kinetics and equilibrium of individual proteins and protein complexes across varied DNA sequences. These techniques provide new analytical tools for the rapid identification of DNA sequence preferences for individual proteins which regulate gene transcription; further, these approaches provide 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. My early work focused on the detection of protein binding in a reagentless, optical manner via the use of surface enhanced resonance Raman spectroscopy (SERRS). In SERRS, the DNA under investigation forms a bridge between two metal nanoparticles, positioning them to allow enhancement of the Raman detection of a protein binding. Later studies optimized this methodology and showed the feasibility of sensitive determination of binding kinetics via this method or by the electrochemical detection of protein binding to and constricting DNA on an electrode surface. The major focus of my work has been on developing and optimizing a microarray-compatible detection strategy that allows the real-time collection of kinetic binding data. This technique has been dubbed TIRF-PBM, for total internal reflectance fluorescence (TIRF) based protein binding microarrays (PBM). This technique has been used to characterize the binding of components of the yeast general transcription factor complex, singly and in complex, across dozens of DNA sequences, establishing equilibrium and kinetic data on the role of multiprotein complexes in specifying DNA specificity. These results correlate well with in vivo studies, and have motivated current work, which focuses on investigating human transcription factors involved in cancer and using TIRF-PBM to screen for potentially selective inhibitory chemotherapeutic drugs. The ultimate goal of my research is to develop an optical protein binding microarray technology for the rapid identification of DNA binding affinities and preferences for proteins and protein complexes involved in genetic regulation.
Publications
Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays
Andrew J. Bonham, Thorsten Neumann, Matthew Tirrell, and Norbert O. Reich
Nucleic Acids Research ASAP Article 10.1093/nar/gkp424 (2009).
Detection of Sequence-Specific Protein-DNA Interactions via Surface Enhanced Resonance Raman Scattering
Andrew J. Bonham, Gary Braun, Ioana Pavel, Martin Moskovits, and Norbert O. Reich
J. Am. Chem. Soc., 129 (47), 14572 -14573, 2007. 10.1021/ja0767837
Reagentless, Electrochemical Approach for the Specific Detection of Double- and Single-Stranded DNA Binding Proteins
Francesco Ricci, Andrew J. Bonham, Aaron C. Mason, Norbert O. Reich, and Kevin W. Plaxco
Anal. Chem., article ASAP, 2009. 10.1021/ac802365x
Presentations
Recent Advances in Bio-Nanotechnology, August 8th, 2007
ASBMB Transcriptional Regulation Meeting, October 18th, 2008
Awards and Honors
George and Joy Rathmann Graduate Fellowship 2004
Kittridge Honors Program 2000-2004
Contact
Reich Lab Contact Info