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    Geometry-based self-assembly of DNA origami-protein hybrid nanostructures

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    Name:
    Hajar Alzarah Thesis.pdf
    Size:
    3.494Mb
    Format:
    PDF
    Description:
    Hajar Al-zarah Thesis
    Embargo End Date:
    2022-07-13
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    Type
    Thesis
    Authors
    Al-Zarah, Hajar A. cc
    Advisors
    Habuchi, Satoshi cc
    Committee members
    Liberale, Carlo cc
    Frøkjær-Jensen, Christian cc
    Program
    Bioscience
    KAUST Department
    Biological and Environmental Science and Engineering (BESE) Division
    Date
    2021-07
    Embargo End Date
    2022-07-13
    Permanent link to this record
    http://hdl.handle.net/10754/670178
    
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    Show full item record
    Access Restrictions
    At the time of archiving, the student author of this thesis opted to temporarily restrict access to it. The full text of this thesis will become available to the public after the expiration of the embargo on 2022-07-13.
    Abstract
    Biological nanomaterials are defined as materials with sizes within the nanoscale range of 1 - 100 nm. The fundamental functionalities and biocompatibility of these materials can be tailored for biotechnology applications. In 1983, Ned Seeman successfully developed the first customized DNA nanostructures, Holliday junctions. Since then, the field has continued to expand rapidly and various 2D and 3D nanostructures has been designed. Although the high predictability of DNA base-pairing is essential for the design of complex DNA nanostructures, it greatly limits its functional versatility; therefore, proteins are conjugated with DNA nanostructures to compensate for that. DNA origami-protein hybrid nanostructures were introduced in 2012. However, the structural units based on DNA origami-protein hybrid nanostructures are still limited, and the majority are constructed by covalent or sequence-specific non-covalent interactions. Here we utilize the inherent, non-sequence-specific interaction between DNA and histones to present sequence-independent self-assembled DNA origami-protein hybrid nanostructures. We demonstrated using various molecular biology and imaging techniques that ssDNAs and histone proteins self-assemble into structurally well-defined complexes. We successfully assembled DNA origami–histone hybrid nanostructures using two different shapes of DNA origami: rectangular (PF-3), and rectangular with central aperture (PF-2) nanostructures. We observed precise localization of nucleosome-like histone-ssDNA nanostructures at the edge (PF-3) or the center (PF-2) of the DNA origami. In addition, we demonstrated that this DNA origami-histone interaction results in the assembly of larger DNA origami complexes, including a head-to-head type dimer and a cross-shape complex. Our results suggest the successful self-assembly of the DNA origami–histone hybrid nanostructures provide a principal structural unit for constructing higher-order nanostructures. Given the reversible nature of the geometry-based noncovalent interaction between the DNA origami and the nucleosome-like histone-ssDNA nanostructures, the self-assembly/disassembly of DNA-histones hybrid nanostructures may open new opportunities to construct stimuli-responsive DNA-protein hybrid nanostructures.
    DOI
    10.25781/KAUST-MC4E6
    ae974a485f413a2113503eed53cd6c53
    10.25781/KAUST-MC4E6
    Scopus Count
    Collections
    Biological and Environmental Science and Engineering (BESE) Division; Bioscience Program; MS Theses

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