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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.

SUBMITTER: Parlea L

PROVIDER: S-EPMC6319925 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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

Parlea Lorena L Bindewald Eckart E Sharan Rishabh R Bartlett Nathan N Moriarty Daniel D Oliver Jerome J Afonin Kirill A KA Shapiro Bruce A BA

Methods (San Diego, Calif.) 20160426

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. ...[more]

PMID: 27090005

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