EFRI CEE: DNA origami tools to engineer chromatin structure and function in live cells

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Numerous organisms from yeast to humans organize their genome by wrapping it repeatedly around histone proteins into nanoscale spools known as chromatin. Cells use the organization of chromatin to dictate whether a gene is actively expressed or turned off. Combining the ability to target a specific gene, visualize its location and structure, activate the gene, and detect gene expression in live cells would be a major technological advance in how genes are studied and controlled in living organisms, and lead to applications in many fields, including medicine, agriculture, energy and the environment. DNA nanotechnology, which uses well-understood folding properties of DNA to engineer nanoscale, biocompatible structures, is an emerging technology with the potential to combine these functions. A 5-PI team will apply bioengineering, cell biology, genetics, single molecule spectroscopy, super resolution microscopy and multi-scale molecular modeling to develop such DNA-based nanodevices that can also operate in live cells and be "switchable" to allow these functions to be triggered at will. The research will be integrated into university curricula, and will enable cross-disciplinary, collaborative and international training of graduate students. The PIs will also broaden participation of underrepresented students in STEM by creating open access standards-based videos and modules for use by K-12 teachers.Recent advances in genetic and epigenetic methods have enabled chromatin engineering technologies that 1) target genes to 2) visualize chromatin structure, 3) activate target genes, and 4) detect gene-specific transcription. However, current tools (including super-resolution imaging, chromatin conformation capture and genome engineering with CRISPR/Cas9) are usually only able to accomplish one of these functions at a time, giving single-channel, static views of the players and processes at a specific transcription site. This project will leverage DNA nanotechnology to leapfrog current technologies for probing and engineering genome and epigenome functions. A team of five PIs will develop multi-functional DNA origami (DO) nanodevices that combine targeting, functional modifications and RNA detection onto a single platform, operate in live cell nuclei, and are "switchable", allowing for real-time detection and for functions to be triggered by endogenous or external signals. The outcomes will serve as a foundation for future automated devices that target and regulate genome and epigenome functions, including gene expression, and serve as diverse new toolsets for science, engineering, and medical applications.This award is co-funded by the Genetic Mechanisms cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate, the Emerging Frontiers in Research and Innovation program in the Division of Emerging Frontiers and Multidisciplinary Activities in the Engineering Directorate, and the Chemistry of Life Processes program in the Division of Chemistry in the Mathematics and Physical Sciences Directorate.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.