title: Complete RNA inverse folding: computational design of functional hammerhead ribozymes.
abstract: Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
authors.forename: Juan Antonio
authors.initials: JA
authors.lastname: Garcia-Martin
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
authors.forename: Betty L
authors.initials: BL
authors.lastname: Slinger
authors.affiliation: Hofstra North Shore-LIJ School of Medicine, Hempstead, NY 11549, USA.
authors.forename: Vinodh
authors.initials: V
authors.lastname: Mechery
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
authors.forename: Michelle M
authors.initials: MM
authors.lastname: Meyer
authors.affiliation: Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA clote@bc.edu.
authors.forename: Peter
authors.initials: P
authors.lastname: Clote
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D016384:Consensus Sequence; D059367:RNA Cleavage; D059370:RNA Folding; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D058615:Synthetic Biology / Q000379:methods
chemical_list: D016337:RNA, Catalytic; C427204:hammerhead ribozyme