3D organization of guest molecules and resolution improvement of self-assembled 3D DNA crystals

Using robust DNA motifs and programmable sticky end cohesion, various self-assembled nano-mechanical devices, nano-objects, 2D or 3D crystals could be generated following the principles of structural DNA nanotechnology. To date no other technology could make similarly precise and large-scale self-assembled nano-materials. This thesis focuses on the 3D organization of gold nanoparticles and protein using a self-assembled 3D DNA crystal, and the improvement of data resolution for self-assembled DNA crystals using a newly designed thermo-control method.;In Chapter 2, the self-assembled DNA crystal-mediated 3D organization of 5 nm, 1.4 nm and 0.8 nm gold nanoparticles are discussed. Different designs of self-assembled DNA crystals with different symmetry and cavity sizes were used to organize gold nanoparticle with different size, and the structures of obtained 3D DNA-gold particle crystals were analyzed using X-ray crystallography method. At the end of this chapter, the design of asymmetric 4 turn DNA triangle motif with helically patterned 1.4 nm gold particles is presented.;In Chapter 3, the slowly-cooling to 4 °C incubation method to improve DNA crystal resolution is studied. By using this incubation method and DNA strands with 5' phosphate group, the resolution of X-ray diffraction data for self-assembled 2 turn tensegrity triangle crystal was improved to 3.23 A and 1.92 A, from previous 4 A resolution; and electron density maps with the highest resolution for this type of crystal were constructed and analyzed. In the end, the experiment design and result for slowly-cooling crystal to -20 °C incubation method are presented.;In Chapter 4, the crystallization and structure of several types of self-assembled DNA crystals are discussed, and all the experiments of using these designs to three-dimensionally organize BamH I protein are summarized. Designs of triangle motifs with the BamH I binding site, crystallization conditions to grow native DNA crystal and to co-crystallize BamH I protein, structure analysis of the native DNA crystals are described in detail in this chapter. A fast incubation method to get small-sized 4 turn triangle crystal for data collection on femtosecond beamline is presented in the end of this chapter.