Programmed Folding of Single-stranded DNA/RNA Nanostructures and the Applications

Mo Li, Purdue University

Abstract

DNA and RNA molecules have drawn great interests from scientists as versatile building materials for nanoconstruction. The field of DNA/RNA nanotechnology has developed rapidly during the past decades and a large variety of well-defined nanostructures have been constructed. Such nano-sized structures are highly programmable with precise structural control. The multifunctional DNA/RNA architectures endow with great potential in model-directed nanofabrication, stimuli-responsive nanodevice and cell-based biomedical applications. However, the traditional tile-based self-assembly strategy is quite limited by available building motifs and structural complexity. So my major researches are aimed at: (1) developing an advanced DNA/RNA strand folding strategy for in-vivo amplification and self-assembly; (2) exploring a new type of inter-tile associations to build novel DNA nanostructures; (3) expanding the variety of DNA motifs by developing a class of DNA building tiles to simply the molecular design. In this thesis, we firstly proposed a programmable single-stranded RNA folding strategy. Several long single RNA strands with different lengths were designed to fold into different nanoparticles. By integrating instinct building elements, a variety of size-precise two dimensional (2D) and three-dimensional (3D) RNA architectures have been constructed through intramolecular assembly process. In addition, a biological system was further applied to confirm that such discrete ssRNA architectures are highly compatible for expression and assembly inside Escherichia coli (E.coli) cells. This stoichiometry independent method could be used to construct well-defined RNA nanostructures in a remarkably high assembly yield, without purification and annealing process. We expect this strategy would benefit the in-vivo biomedical applications of RNA nanotechnology. Besides RNA nanoparticle assembly, we also studied the DNA bubble-bubble interactions in DNA nanostructure constructions. The well-designed DNA bubble sequence was applied into the nanomotifs so that the traditional sticky-ends cohesion could be circumvented. By applying a sequence symmetry strategy, the nanomotifs design is simplified that it only contains one single DNA strand. One-component DNA 1D ladder, 2D periodic array and 3D nanoprism have been successfully constructed in a remarkably high yield. Bubble-bubble cohesion is like a DNA version of RNA kissing-loop interaction. Both the molecular design and self-assembly of DNA tiles can be simplified by utilizing DNA bubbles. Finally, a class of DNA nanomotifs that provide high connectivities in DNA nanoconstruction was reported. The design of DNA double multi-arm junction (DMaJ) nanomotifs was inspired by canonical DNA Double-crossover (DX) molecule. Each motif contains two multi-arm junctions, connected as pseudo-continuous DNA double duplexes. The motifs connect with each other to form long 1D chains or large 2D frameworks through the hybridization of sticky-ends, which were added onto the parallel DNA helices The assembly behaviors of these novel motifs have been thoroughly characterized by polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) imaging.

Degree

Ph.D.

Advisors

Mao, Purdue University.

Subject Area

Analytical chemistry|Biochemistry|Nanotechnology

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