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Methods. 2016 Jul 1;103:128-37. doi: 10.1016/j.ymeth.2016.04.016. Epub 2016 Apr 26.

Ring Catalog: A resource for designing self-assembling RNA nanostructures.

Author information

1
Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
2
Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
3
Department of Chemistry, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC 28223, USA.
4
Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: shabirbr@mail.nih.gov.

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.

KEYWORDS:

3D structural elements; Nanoconstruct; RNA motifs; RNA nanoparticle; Self-assembly; Sequence design

PMID:
27090005
PMCID:
PMC6319925
DOI:
10.1016/j.ymeth.2016.04.016
[Indexed for MEDLINE]
Free PMC Article

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