Nanomedicine Center for Nucleoprotein Machines

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Nucleoprotein machines carry out essential biological processes including synthesis, modification, and repair of DNA and RNA. We propose to establish a nanomedicine development center (NDC) focusing on a model nanomachine that carries out nonhomologous end joining (NHEJ) of DNA double strand breaks. This and other DNA repair machines have relatively simple structures (< 20 components) and significant biological and clinical relevance. DNA damage repair is vitally important to human health, as both normal metabolic activities and environmental factors can cause DNA damage, resulting in as many as 100,000 individual molecular lesions per cell per day. If allowed to accumulate without repair, these lesions interfere with gene transcription and replication, leading to premature aging, apoptosis, or unregulated cell division. We have assembled an interdisciplinary team from eight institutions, with significant expertise in cell and molecular biology of DNA damage repair, protein tagging and targeting, nanostructured probes, cryo-electron microscopy, signal-cell imaging, quantitative image analysis and computational biology, and light microscopy instrumentation. We will develop innovative nanotechnologies and biomolecular approaches to elucidate the structure-function relationships within and among DNA repair nanomachines. General principles emerging from these studies will lay a foundation for precise modification of the information stored in DNA and RNA, leading ultimately to novel therapeutic strategies for a wide range of diseases, including cancer. The NDC has five closely related aims including: (1) to develop orthogonal protein tagging strategies and novel fluorescence probes including quantum dot bioconjugates for nanomachine targeting; (2) to decipher structure-function relationship of components required for the core NHEJ reaction; (3) to characterize the dynamics of nanomachine assembly and disassembly in the context of repair foci; (4) to determine the dimensions and structure of repair foci at high resolution in fixed cells; (5) to establish the engineering design principles underlying DNA double-strand break repair. This NDC will complement existing NDCs that focus on filaments, membranes and protein folding enzymes, and the probes, tools and methodologies developed will be applicable to a wide range of biological and disease studies. Our long-term vision is to provide genetic cures for common human diseases based on the ability to manipulate the somatic human genome using nanomedicine approaches that are inexpensive, effective, and user-friendly, similar to vaccination today.