title: Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript.
abstract: We present a new publicly accessible web-service, RiboSoft, which implements a comprehensive hammerhead ribozyme design procedure. It accepts as input a target sequence (and some design parameters) then generates a set of ranked hammerhead ribozymes, which target the input sequence. This paper describes the implemented procedure, which takes into consideration multiple objectives leading to a multi-objective ranking of the computer-generated ribozymes. Many ribozymes were assayed and validated, including four ribozymes targeting the transcript of a disease-causing gene (a mutant version of PABPN1). These four ribozymes were successfully tested in vitro and in vivo, for their ability to cleave the targeted transcript. The wet-lab positive results of the test are presented here demonstrating the real-world potential of both hammerhead ribozymes and RiboSoft. RiboSoft is freely available at the website http://ribosoft.fungalgenomics.ca/ribosoft/.
authors.affiliation: Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada kharma@ece.concordia.ca.
authors.forename: Nawwaf
authors.initials: N
authors.lastname: Kharma
authors.affiliation: Biology Department, Concordia University, 7141 rue Sherbrooke O., Montreal, QC, H4B 1R6, Canada.
authors.forename: Luc
authors.initials: L
authors.lastname: Varin
authors.affiliation: Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada.
authors.forename: Aida
authors.initials: A
authors.lastname: Abu-Baker
authors.affiliation: INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Ouellet
authors.affiliation: INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
authors.forename: Sabrine
authors.initials: S
authors.lastname: Najeh
authors.affiliation: Biology Department, Concordia University, 7141 rue Sherbrooke O., Montreal, QC, H4B 1R6, Canada.
authors.forename: Mohammad-Reza
authors.initials: MR
authors.lastname: Ehdaeivand
authors.affiliation: Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Belmonte
authors.affiliation: Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada.
authors.forename: Anas
authors.initials: A
authors.lastname: Ambri
authors.affiliation: Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada.
authors.forename: Guy
authors.initials: G
authors.lastname: Rouleau
authors.affiliation: INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada jonathan.perreault@iaf.inrs.ca.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Perreault
mesh_terms: D005786:Gene Expression Regulation; D006801:Humans; D009690:Nucleic Acid Conformation; D039122:Poly(A)-Binding Protein I / Q000235:genetics* / Q000378:metabolism; D016337:RNA, Catalytic / Q000235:genetics* / Q000302:isolation & purification; D014158:Transcription, Genetic
chemical_list: C576588:PABPN1 protein, human; D039122:Poly(A)-Binding Protein I; D016337:RNA, Catalytic; C427204:hammerhead ribozyme