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Research Areas Bioorganic Chemistry, Fluorescent Dyes, DNA Nanotechnology, Molecular Evolution, Peptide Nucleic Acids, Molecular Recognition of DNA/RNA, G Quadruplexes The Armitage group works on projects at the interface of organic chemistry with biological and materials sciences. Our research benefits from collaborative interactions with scientists in two large centers at CMU, the Molecular Biosensor and Imaging Center (MBIC, www.mbic.cmu.edu) and the Center for Nucleic Acids Science and Technology (CNAST, www.cmu.edu/cnast). Both of these interdisciplinary research centers integrate chemistry with molecular and cell biology, providing students with the opportunity to learn a broad portfolio of techniques. Specific projects and collaborations are described below. 1. Bright Fluorescent Labels Based on DNA Nanostructures In this project, we use 1D, 2D and 3D DNA nanostructures as scaffolds for the assembly of fluorescent dye arrays. The DNA allows us to concentrate large numbers of dyes within small volumes of space without allowing self-quenching of the dyes. We rely on synthetic organic chemistry to prepare these “DNA nanotags” and then characterize their fluorescence properties by spectroscopy, time-resolved lifetime measurements, single molecule analysis, flow cytometry and microscopy. We collaborate with the Peteanu group on the characterization experiments and with two groups from the Department of Biological Sciences led by Brooke McCartney and Javier Lopez to apply nanotag labels for intracellular protein and RNA detection. 2. Fluoromodules: A New Class of Fluorescence Imaging Agents Based on Dye-Protein Complexes The goal of this project is to create a catalogue of fluorescent dye-protein complexes that can be used as genetically encodable labels and biosensors for imaging and detection assays. These “fluoromodules” consist of fluorogenic dyes, i.e. dyes that are nonfluorescent in solution, but become fluorescent when conformationally constrained in some way, and specific protein partners that bind to the dye noncovalently, but with high affinity, leading to strong fluorescence from the dye. Synthetic organic chemistry is used to prepare the fluorogenic dyes, while the protein partners are selected from a library consisting of one billion distinct protein molecules. Once an appropriate protein has been isolated from the library for both strong binding and bright fluorescence activation, the “fluorogen-activation protein”, or FAP, can be genetically fused to a protein of interest. When the protein is expressed inside of a cell or at the cell surface, addition of the fluorgenic dye gives a fluorescent signal to the protein, which can then be imaged and tracked using fluorescence microscopy. This project is part of a larger effort in MBIC that includes significant support from the NIH’s National Technology Centers for Networks and Pathways program. We collaborate closely with Alan Waggoner and Peter Berget of the Department of Biological Sciences and MBIC. 3. DNA and RNA Recognition by G Quadruplex-Forming Peptide Nucleic Acids Peptide nucleic acids (PNAs) are synthetic mimics of DNA/RNA in which the hydrogen bonding bases (G,A,C and T) are attached to a peptide-like backbone. Thus, PNA is a chimeric molecule with properties that are reminiscent of both natural proteins and nucleic acids. One of the unique strengths of our department is its development of peptide nucleic acids (PNAs) for applications ranging from chemical biology and biotechnology to nanotechnology and molecular electronics. In most cases, PNAs are designed to have sequences that are complementary to a given DNA or RNA target, allowing the PNA to form a double-helical complex with the target via Watson-Crick base pairing. In collaboration with Danith Ly’s group, we have been designing a special class of PNAs that form “guanine quadruplexes” with specific DNA and RNA targets. This binding mode relies on the PNA and the target nucleic acid to have similar, guanine-rich sequences. Recognition still relies on hydrogen-bond formation, but instead of a G-C pair, the basic unit is a G tetrad, in which the PNA and the DNA/RNA each provide two guanines to a given tetrad. The G-rich target sequences in DNA and RNA have profound biological importance, having been implicated in the regulation of gene expression in diseases ranging from cancer to malaria. Thus, targeting PNAs to these regions should interfere with gene expression, providing important chemical tools for understanding the molecular basis for these diseases and potential therapeutics. We collaborate with Danith Ly on this project.