Significance of Knotted Structures for Function of Proteins and Nucleic Acids
Saturday Abstracts
Single-Stranded Architecture for Cotranscriptional Folding of RNA Nanostructures
Cody Geary
1
, Paul Rothemund
2
,
Ebbe Andersen
1
.
1
Aarhus University, Aarhus, Denmark,
2
California Institute of Technology, Pasadena, CA, USA.
RNA nanotechnology uses the diversity of structural and functional modules from natural RNA
molecules to engineer novel nanoscale devices. An important goal is to be able to design large
and well-defined RNA structures that can assemble during the transcription process, since such
structures can be genetically encoded and expressed in cells with diverse applications in
synthetic biology. Here, we introduce a general architecture for designing artificial RNA
structures that can fold from a single strand: Arrays of antiparallel RNA helices are precisely
organized by RNA pseudoknot motifs and a new type of crossover pattern that can fold without
topological problems. To validate our architecture we construct RNA tiles that assemble into
hexagonal lattices, and demonstrate that lattices can be made by annealing and/or
cotranscriptional folding. We further show that the tiles can be scaled up to 660 nucleotides in
length, reaching a size comparable to that of large natural ribozymes. We conclude that the
folding path of complex RNA nanostructures can be rationally designed and will discuss the
geometric principles, structure prediction algorithms, and kinetic folding models that are
required to extend this design paradigm further.
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