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  1. Article ; Online: 3D RNA-scaffolded wireframe origami.

    Parsons, Molly F / Allan, Matthew F / Li, Shanshan / Shepherd, Tyson R / Ratanalert, Sakul / Zhang, Kaiming / Pullen, Krista M / Chiu, Wah / Rouskin, Silvi / Bathe, Mark

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 382

    Abstract: Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, ... ...

    Abstract Hybrid RNA:DNA origami, in which a long RNA scaffold strand folds into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterize secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.
    MeSH term(s) Nanotechnology/methods ; RNA ; Cryoelectron Microscopy ; Nucleic Acid Conformation ; Nanostructures/chemistry ; RNA, Messenger
    Chemical Substances RNA (63231-63-0) ; RNA, Messenger
    Language English
    Publishing date 2023-01-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-36156-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami.

    Jun, Hyungmin / Wang, Xiao / Parsons, Molly F / Bricker, William P / John, Torsten / Li, Shanshan / Jackson, Steve / Chiu, Wah / Bathe, Mark

    Nucleic acids research

    2021  Volume 49, Issue 18, Page(s) 10265–10274

    Abstract: Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While ... ...

    Abstract Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.
    MeSH term(s) DNA/chemistry ; Gold/chemistry ; Metal Nanoparticles/chemistry ; Nanostructures/chemistry ; Nanotechnology/methods ; Nucleic Acid Conformation ; Software
    Chemical Substances Gold (7440-57-5) ; DNA (9007-49-2)
    Language English
    Publishing date 2021-09-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab762
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Article ; Online: Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami.

    Chen, Chi / Wei, Xingfei / Parsons, Molly F / Guo, Jiajia / Banal, James L / Zhao, Yinong / Scott, Madelyn N / Schlau-Cohen, Gabriela S / Hernandez, Rigoberto / Bathe, Mark

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4935

    Abstract: Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their ... ...

    Abstract Control over the copy number and nanoscale positioning of quantum dots (QDs) is critical to their application to functional nanomaterials design. However, the multiple non-specific binding sites intrinsic to the surface of QDs have prevented their fabrication into multi-QD assemblies with programmed spatial positions. To overcome this challenge, we developed a general synthetic framework to selectively attach spatially addressable QDs on 3D wireframe DNA origami scaffolds using interfacial control of the QD surface. Using optical spectroscopy and molecular dynamics simulation, we investigated the fabrication of monovalent QDs of different sizes using chimeric single-stranded DNA to control QD surface chemistry. By understanding the relationship between chimeric single-stranded DNA length and QD size, we integrated single QDs into wireframe DNA origami objects and visualized the resulting QD-DNA assemblies using electron microscopy. Using these advances, we demonstrated the ability to program arbitrary 3D spatial relationships between QDs and dyes on DNA origami objects by fabricating energy-transfer circuits and colloidal molecules. Our design and fabrication approach enables the geometric control and spatial addressing of QDs together with the integration of other materials including dyes to fabricate hybrid materials for functional nanoscale photonic devices.
    MeSH term(s) Coloring Agents ; DNA/chemistry ; DNA, Single-Stranded ; Nanostructures/chemistry ; Quantum Dots/chemistry
    Chemical Substances Coloring Agents ; DNA, Single-Stranded ; DNA (9007-49-2)
    Language English
    Publishing date 2022-08-23
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-32662-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Programming Structured DNA Assemblies to Probe Biophysical Processes.

    Wamhoff, Eike-Christian / Banal, James L / Bricker, William P / Shepherd, Tyson R / Parsons, Molly F / Veneziano, Rémi / Stone, Matthew B / Jun, Hyungmin / Wang, Xiao / Bathe, Mark

    Annual review of biophysics

    2019  Volume 48, Page(s) 395–419

    Abstract: Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target ...

    Abstract Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
    MeSH term(s) Biomimetics ; Biophysics/methods ; DNA/chemistry ; DNA/metabolism ; RNA/chemistry ; RNA/metabolism ; Receptors, Immunologic/metabolism ; Signal Transduction
    Chemical Substances Receptors, Immunologic ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2019-05-11
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 2434725-5
    ISSN 1936-1238 ; 1936-122X
    ISSN (online) 1936-1238
    ISSN 1936-122X
    DOI 10.1146/annurev-biophys-052118-115259
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Se 190: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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