Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

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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