Engineering Bioimaging Probes Based on Triggered Molecular Geometry

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DESCRIPTION (Provided by the applicant) Abstract: Microscopy is a central tool for studying biology. At the heart of microscopic technology is the imaging probe, which transduces invisible biological information to an imageable signal. Present imaging probes are mostly engineered by manipulating their optical, chemical, and physical properties. But modern microscopy's ever in- creasing power to resolve shape, and nanotechnology's power to precisely engineer shape are creating a striking opportunity for a new kind of probes based on "engineered geometry". We propose to engineer imaging probes based on "triggered molecular geometry": upon detecting a molecular signal, the probe produces a prescribed, imageable molecular shape. Our probe consists of metastable nucleic acid monomers. Only upon detecting a target biomolecule, they autonomously self-assemble into a programmable 3D structure with prescribed geome- try. The shape can be imaged directly; alternatively, it can serve as a spatial organizer or amplification scheme for other imaging entities. To achieve this goal, we will build on our recent success in engineering nucleic acid self- assembly pathways to develop a new paradigm in synthetic molecular self-assembly, where a synthetic molecular structure grows isothermally, following explicitly designed kinetic pathways. This new paradigm is fundamen- tally different from and conceptually more powerful than the present thermal annealing based paradigm, and is uniquely suitable for implementing triggered-molecular-geometry for biomedical applications. To demonstrate its power, we will build probes for three enabling bioimaging applications: (1) a triggered fluorescent geometric bar- code for the simultaneous imaging of many distinct mRNA species, (2) a protein organizer that will make present fluorescent protein technology much more flexible, expressive, and easier to use, and (3) a triggered geometric barcode as a long sought-after visual marker for electron cryotomography. If successful, the proposed work will allow geometry to join optics, chemistry, and physics as a fundamental, engineerable property for constructing imaging probes, with profound scientific and medical implications. Public Health Relevance: We propose to engineer bioimaging probes based on triggered molecular geometry. The probe produces a prescribed, imageable 3D shape upon detecting a target biomolecular signal. If successful, the proposed work will allow geometry to join optics, chemistry, and physics as a fundamental, engineerable property for constructing imaging probes, with profound scientic and medical implications.