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

Student thesis: Master's Thesis


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.
Date of AwardJul 2021
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorSatoshi Habuchi (Supervisor)


  • DNA origami
  • geometry-based
  • self-assembly
  • histone protein
  • nanostructure
  • DAN-protein hybrid

Cite this