Abstract:
RNA nanotechnology is rapidly emerging field and has recently received wide interest in
the scientific community. The field is focused on design, synthesis, and assembly of artificial
RNA nanoparticles with wide
spectra applications in synthetic
biology and medicine (1,2). This
work demonstrates the robust
properties of in-silico designed
RNA tetra-uracil (tetra-U)
structural 3D motifs for the
construction of nanometer-scale
nucleic acid geometries (Figure
1). The artificial tetra-U motif is unique and advantageous to the previous reports (3,4) in that it
possesses the special property of self-assembly and can be controlled to predictably build
structures of defined size, shape, and stoichiometry. Particularly, we demonstrate the fabrication
of economically favorable RNA triangular nano-scaffolds based on RNA, DNA, and hybrid
2
RNA-DNA strands, the geometries of which were confirmed by atomic force microscope. Each
of the triangle nanoparticles was thoroughly analyzed and their physicochemical properties were
compared using well-established assays, including UV-melting, enzymatic degradation,
immunostimulatory activity, and gene-silencing implementing RNAi technology. We found that
the modulation of RNA and DNA strand composition makes it possible to engineer, in a de novo
fashion, nanometer-scaled particles that are enzymatically resistant, thermodynamically stable,
and potentially instrumental in the delivery of fluorescent probes and gene-silencing agents to
cancer cells. Furthermore, the triangular nano-scaffolds show great promise for biomedical
applications due to their tunable immunostimulatory properties.
Overall, the system shown here for a simple design to precisely tune physicochemical and
biostimulatory properties adds a new angle to exploiting RNA/DNA hybrid nanoparticles in a
clinical setting. We have also obtained preliminary data demonstrating that tetra-U motif can be
used to construct other polygons made of RNA and DNA including squares, pentagons, and
hexagons. Further work is currently under investigation. We are planning to evaluate nucleic
acid polygon’s physicochemical properties including assembly efficiency at isothermal
conditions, thermodynamic stabilities, and enzymatic resistance. This data will be crucial to
further demonstrate the importance of such economically advantageous and fine-tunable hybrid
RNA/DNA nanostructures to fulfill the needs of the rapidly developing field of RNA
nanotechnology.
