{"@context":"http://iiif.io/api/presentation/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/manifest.json","@type":"sc:Manifest","label":"DNA-programmable Nano-systems: Design, Reconfiguration and Optical Properties","metadata":[{"label":"dc.description.sponsorship","value":"This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree."},{"label":"dc.format","value":"Monograph"},{"label":"dc.format.medium","value":"Electronic Resource"},{"label":"dc.identifier.uri","value":"http://hdl.handle.net/11401/77075"},{"label":"dc.language.iso","value":"en_US"},{"label":"dc.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.abstract","value":"One of the main goals of nanotechnology is developing methods for creation of designed nano-scaled systems with ability to control their structures, transformations and dynamic processes. Such full control over the material design will permit achieving the desired functional properties. Approaches based on DNA-driven assembly of nanosystems were recently demonstrated as a powerful route for regulated self-assembly at nanoscale. Metal nanoparticles or quantum dots, functionalized with oligonucleotides are envisioned in this approach to be precisely directed in targeted structures, in bulk, at surfaces or within a cluster.  The Watson-Crick recognition between DNA grafted on particle surface allows for programming interparticle interactions with extreme richness and thermodynamical tunability.   Firstly, we extended DNA-assembly methodology for fabrication of dynamically responsive clusters, which were switched between dimer (two-particle) and trimer (three-particle) structures. We developed a simple yet effective approach for the switching the morphology of nanoparticle clusters using a linking particles \u2018i-motif\u2019, a DNA sequence that responds to pH stimulation. Our experiments demonstrate that such cluster switching can be reversibly cycled multiple times. Moreover, by employing both gold nanoparticles (NP) and fluorescent quantum dots, we showed that structural cluster switching induced corresponding changes in the system optical response due to the fluorescence quenching by plasmonic particle. Then, we successfully fabricated three-dimensional superlattices using the \u2018i-motif\u2019 sequence as a linker. Our in-situ synchrotron-based small angle x-ray scattering (SAXS) measurements revealed repeatable lattice transformations for the formed body centered cubic (bcc) superlattices. We also uncovered changes in the interparticle distances during pH cycling of simple more complex DNA motifs.  Secondly, we used the DNA-driven assembly strategy to self-assemble a series of clusters with core-shell architecture. The core, gold nanoparticle (AuNP) was surrounded by the shell of DNA-attached colloidal quantum dots (QD), forming AuNP-DNA-QD clusters with tunable optical (photoluminescence) responses, which mimics the architecture of light harvesting complex. By varying the inter-component distance through the DNA linker length we demonstrated precise biasing of the plasmon-exciton interactions, and as such of the optical response of the nanoclusters from photoluminescence quenching to about five-fold enhancement.  Thirdly, considering that DNA sequence has chiral structure, its functionalization onto the surface of plasmonic nanoparticles was predicted theoretically to induce the circular Dichroism (CD) signal in plasmonic area. This effect was observed previously but no significant amplification was detected. However, we demonstrated that for silver nanocube about two orders of magnitudes enhancement of CD signal can be induced. We also confirmed that orientation of DNA played an important role in determining the magnitude of the response.  Furthermore, we reported a novel strategy for assembling 3D nanoparticle clusters: designing a molecular frame with encoded vertices for particles placement. Using a DNA origami octahedron as such frame we positioned specific particles types at the octahedron vertices, which permitted a fabrication of clusters with different symmetries and particles composition. We applied the combination of cryo-EM technique and single particle method to uncover the structure of the DNA frame and to reveal that nanoparticles are spatially coordinated in the prescribed manner. Our strategy is advantageous for nanomaterial engineering because it permits massive and precise assembly of mesoscale 3D clusters by-design. Plasmonic chiral signal can be induced by positioning NP in the desired way. Lastly, we proposed a new strategy for creating prescribed NP superlattices via coupling DNA frames and NPs into DNA-NP frameworks. We designed several typical frames of polyhedra including cube, square dipyramid, prism, tetrahedron and their variations as the building block for construction of 3-D crystals. Gold nanoparticle, with functional sticky ends on the entire surface, can be treated as \u2018universal glue\u2019 for the assembly process. We investigated conditions and designed parameters that lead to the formation ordered DNA-NP frameworks. Using SAXS characterization we reveal several types of well-ordered structures for the frameworks. By programming the DNA frame, we precisely control the positions and numbers of functional DNA sticky ends that permits regulating the topology of connections and result in the formation of different types of arrays."},{"label":"dcterms.available","value":"2017-09-20T16:51:51Z"},{"label":"dcterms.contributor","value":"Grubbs, Robert"},{"label":"dcterms.creator","value":"Tian, Ye"},{"label":"dcterms.dateAccepted","value":"2017-09-20T16:51:51Z"},{"label":"dcterms.dateSubmitted","value":"2017-09-20T16:51:51Z"},{"label":"dcterms.description","value":"Department of Chemistry."},{"label":"dcterms.extent","value":"190 pg."},{"label":"dcterms.format","value":"Monograph"},{"label":"dcterms.identifier","value":"http://hdl.handle.net/11401/77075"},{"label":"dcterms.issued","value":"2015-05-01"},{"label":"dcterms.language","value":"en_US"},{"label":"dcterms.provenance","value":"Made available in DSpace on 2017-09-20T16:51:51Z (GMT). No. of bitstreams: 1\nTian_grad.sunysb_0771E_12263.pdf: 7509304 bytes, checksum: 53a296eb73a18e883d7e166dab7445ba (MD5)\n  Previous issue date: 2015"},{"label":"dcterms.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.subject","value":"Chemistry"},{"label":"dcterms.title","value":"DNA-programmable Nano-systems: Design, Reconfiguration and Optical Properties"},{"label":"dcterms.type","value":"Dissertation"},{"label":"dc.type","value":"Dissertation"}],"description":"This manifest was generated dynamically","viewingDirection":"left-to-right","sequences":[{"@type":"sc:Sequence","canvases":[{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json","@type":"sc:Canvas","label":"Page 1","height":1650,"width":1275,"images":[{"@type":"oa:Annotation","motivation":"sc:painting","resource":{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/12%2F20%2F60%2F12206071710127555239478470386024174322/full/full/0/default.jpg","@type":"dctypes:Image","format":"image/jpeg","height":1650,"width":1275,"service":{"@context":"http://iiif.io/api/image/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/12%2F20%2F60%2F12206071710127555239478470386024174322","profile":"http://iiif.io/api/image/2/level2.json"}},"on":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json"}]}]}]}