title: Ring Catalog: A resource for designing self-assembling RNA nanostructures.
abstract: Designing self-assembling RNA ring structures based on known 3D structural elements connected via linker helices is a challenging task due to the immense number of motif combinations, many of which do not lead to ring-closure. We describe an in silico solution to this design problem by combinatorial assembly of RNA 3-way junctions, bulges, and kissing loops, and tabulating the cases that lead to ring formation. The solutions found are made available in the form of a web-accessible Ring Catalog. As an example of a potential use of this resource, we chose a predicted RNA square structure consisting of five RNA strands and demonstrate experimentally that the self-assembly of those five strands leads to the formation of a square-like complex. This is a demonstration of a novel "design by catalog" approach to RNA nano-structure generation. The URL https://rnajunction.ncifcrf.gov/ringdb can be used to access the resource.
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Lorena
authors.initials: L
authors.lastname: Parlea
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
authors.forename: Eckart
authors.initials: E
authors.lastname: Bindewald
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Rishabh
authors.initials: R
authors.lastname: Sharan
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Bartlett
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Moriarty
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
authors.forename: Jerome
authors.initials: J
authors.lastname: Oliver
authors.affiliation: Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA.
authors.forename: Kirill A
authors.initials: KA
authors.lastname: Afonin
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: shabirbr@mail.nih.gov.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D030561:Databases, Nucleic Acid; D019281:Dimerization; D049329:Nanostructures; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software
chemical_list: D012313:RNA
keywords: 3D structural elements; Nanoconstruct; RNA motifs; RNA nanoparticle; Self-assembly; Sequence design