title: Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots.
abstract: We are presenting NanoFolder, a method for the prediction of the base pairing of potentially pseudoknotted multistrand RNA nanostructures. We show that the method outperforms several other structure prediction methods when applied to RNA complexes with non-nested base pairs. We extended this secondary structure prediction capability to allow RNA sequence design. Using native PAGE, we experimentally confirm that four in silico designed RNA strands corresponding to a triangular RNA structure form the expected stable complex.
authors: Basic Science Program, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland, United States.
authors: Eckart
authors: E
authors: Bindewald
authors: Kirill
authors: K
authors: Afonin
authors: Luc
authors: L
authors: Jaeger
authors: Bruce A
authors: BA
authors: Shapiro
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*; D009690:Nucleic Acid Conformation; D010316:Particle Size; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*; D013499:Surface Properties
chemical_list: D012313:RNA