1
|
Kharma N, Varin L, Abu-Baker A, Ouellet J, Najeh S, Ehdaeivand MR, Belmonte G, Ambri A, Rouleau G, Perreault J. Automated design of hammerhead ribozymes and validation by targeting the PABPN1 gene transcript. Nucleic Acids Res 2015; 44:e39. [PMID: 26527730 PMCID: PMC4770207 DOI: 10.1093/nar/gkv1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/12/2015] [Indexed: 12/23/2022] Open
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/.
Collapse
Affiliation(s)
- Nawwaf Kharma
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Luc Varin
- Biology Department, Concordia University, 7141 rue Sherbrooke O., Montreal, QC, H4B 1R6, Canada
| | - Aida Abu-Baker
- Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Jonathan Ouellet
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Sabrine Najeh
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | | | - Gabriel Belmonte
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Anas Ambri
- Electrical & Computer Eng. Dept., Concordia University, 1455 boul. de Maisonneuve O., Montreal, QC, H3G 1M8, Canada
| | - Guy Rouleau
- Montreal Neurological Hospital and Institute, 3801 University Street, Montreal, QC, H3A 2B4, Canada
| | - Jonathan Perreault
- INRS - Institut Armand-Frappier, 531 boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| |
Collapse
|
2
|
Lévesque MV, Rouleau SG, Perreault JP. Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 2011; 21:241-52. [PMID: 21793786 DOI: 10.1089/nat.2011.0301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a specific on/off adaptor (specifically the SOFA-HDV ribozymes) which greatly increases both the ribozyme's specificity and its cleavage activity. Unlike RNAi and hammerhead ribozymes, the designing of SOFA-HDV ribozymes to cleave, in trans, given RNA species has never been the object of a systematic optimization study, even with their recent use for the gene knockdown of various targets. This report aims at both improving and clarifying the design process of SOFA-HDV ribozymes. Both the ribozyme and the targeted RNA substrate were analyzed in order to provide new criteria that are useful in the selection of the most potent SOFA-HDV ribozymes. The crucial features present in both the ribozyme's biosensor and blocker, as well as at the target site, were identified and characterized. Simple rules were derived and tested using hepatitis C virus NS5B RNA as a model target. Overall, this method should promote the use of the SOFA-HDV ribozymes in a plethora of applications in both functional genomics and gene therapy.
Collapse
Affiliation(s)
- Michel V Lévesque
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , Sherbrooke, Québec, Canada
| | | | | |
Collapse
|
3
|
Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
Collapse
Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| |
Collapse
|