Design and Visualization of DNA/RNA Nanostructures from Branched Oligonucleotides Using Blender Software

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

“…In the experiment with the complementary starlet F, the TEM images revealed numerous discrete nanostructures of the size of ca. 35 nm predicted by the modeling [46], which display the same hexagonal pattern with a central core as in the model in Figure 3. When the control starlet F* lacking complementarity to the template was used, the outcome was drastically different, with almost no discrete objects observed apart from what looked like isolated templates with no shells and a lot of unstructured material, likely resulting from uncontrolled polymerization of F* in the absence of the template.…”

“…Using Blender, relatively simple yet informative models of DNA tetrahedron and DNA cube were previously obtained with the selected parameters [47], followed by a more complex model of a C24 fullerene-like DNA shell in the current work (Figure 3). It turned out that Blender is well suited for the visualization of nanostructures such as these and for selecting parameters that allow for their assembly without obvious spatial strain [46,47].…”

“…We previously hypothesized [46] that the complex of the DNA shell with the hybrid DNA/RNA template may serve as a delayed action RNA interference (RNAi) agent if the internal duplexes of the template 2:3 and 4:5 (Figure 2) were constructed as small interfering RNAs (siRNAs). It was shown that some branched RNAs showed biological activity according to RNAi mechanism [56].…”

“…The task can be achieved by hybridization to a specifically formed branched oligonucleotidic template serving as an internal 3D scaffold to support the shape of the target polyhedron, e.g., tetrahedron, cube, octahedron, etc. [46]. The method of choice for obtaining the corresponding branched oligonucleotides seemed to be a combination of automated solid-phase synthesis using, apart from nucleoside phosphoramidites, non-nucleosidic phosphoramidites of specific functionality, such as doublers, treblers, or cleavable linkers, followed by either post-synthetic ligation in solution, e.g., via click chemistry, or a Watson-Crick hybridization to form supramolecular noncovalent assemblies.…”

“…Initially, we have justified via calculations and molecular modeling a set of oligonucleotide sequences for the branched oligonucleotidic templates for the assembly of a DNA tetrahedron, a DNA cube, and a DNA hollow shell analogous to C 24 fullerene. Simultaneously, a 4-way junction oligonucleotidic building block (nicknamed by us as starlet) common to all three above topologies was selected [46]. Commercially available nonnucleosidic branching phosphoramidites (symmetric doubler and trebler) and modifying phosphoramidites (e.g., C6 disulfide linker) were employed for the synthesis of the templates and the starlet.…”