Investigating and Reprogramming RNA Folding with Molecular Probes by Allan, Matthew F.

“…First, a method of nucleic acid origami is developed in which four divergent RNA sequences are reprogrammed by short antisense oligonucleotides (ASOs) to fold into six different 3D wireframe polyhedra. How each type of structural feature in the polyhedra affects the stability of local base pairs is revealed using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq). …”
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Methods to program and to probe RNA tertiary structure with nucleic acid origami by Parsons, Molly F.

“…The resulting algorithm for designing RNA-scaffolded polyhedra enables precise, covalent anchoring of a target RNA fragment onto a wireframe polyhedra. …”
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3D RNA-scaffolded wireframe origami by Parsons, Molly F, Allan, Matthew F, Li, Shanshan, Shepherd, Tyson R, Ratanalert, Sakul, Zhang, Kaiming, Pullen, Krista M, Chiu, Wah, Rouskin, Silvi, Bathe, Mark

“…Here, we investigate design principles of three-dimensional wireframe RNA-scaffolded origami rendered as polyhedra composed of dual-duplex edges. We computationally design, fabricate, and characterize tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. …”
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Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami by Jun, Hyungmin, Wang, Xiao, Parsons, Molly F, Bricker, William P, John, Torsten, Li, Shanshan, Jackson, Steve, Chiu, Wah, Bathe, Mark

“…Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. …”
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Automated Sequence Design of 3D Polyhedral Wireframe DNA Origami with Honeycomb Edges by Jun, Hyungmin, Shepherd, Tyson R, Zhang, Kaiming, Bricker, William P, Bathe, Mark

“…As an alternative, here we introduce the scaffolded DNA origami sequence design algorithm TALOS, which is a generalized procedure for the fully automated design of wireframe 3D polyhedra composed of edges of any cross section with an even number of duplexes, and apply it to DNA-NPs composed uniformly of single honeycomb edges. …”
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