Education

BSc, University of Sherbrooke

Ph.D., University of Sherbrooke

Research Interests

RNA Function:

1. Creation of RNA aptamers by different SELEX (systematic evolution of ligands by exponential enrichment) methods.
2. Fusion of RNA aptamer modules to engineer artificial riboswitch.
3. Bioinformatics and structural studies of the WNV (West Nile virus) UTRs (untranslated region).

Scholarly Articles

1.      Bussière^# F, Ouellet^# J, Côté F, Lévesque D and Perreault JP. Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex, branched secondary structure.^# These authors have an equal contribution.  Journal of Virology. 74 (6) 2647-54 (2000) . 

2.      Pelchat M, Lévesque D, Ouellet J, Laurendeau S, Lévesque S, Lehoux J, Thompson DA, Skrzeckowski LJ and Perreault JP.  Sequencing of peach latent mosaic viroid variants from nine North American peach cultivars shows that this RNA folds into a complex secondary structure.   Virology. 27 37-45 (2000) .  

3.      Ananvoranich S, Fiola K, Ouellet J, Deschênes P and Perreault, JP.  Kinetic analysis of a bimolecular hepatitis delta ribozyme.  Methods in Enzymology. 341 553-6 (2001).  

4.      Deschênes^# P, Ouellet^# J, Perreault^#J, Perreault JP.  Formation of the P1.1 pseudoknot is critical for both the cleavage activity and substrate specificity of an antigenomic trans-acting hepatitis delta ribozyme. ^# These authors have an equal contribution.  Nucleic Acids Research. 15;31(8):2087-96 (2003).  

5.      Bergeron^# LJ, Ouellet^# J and Perreault JP.  Ribozyme-based gene-inactivation system require a fine comprehension of their substrate specificity; the case of delta ribozyme. ^# These authors have an equal contribution.  Current Medicinal Chemistry. 10(23):2589-97 (2003).  

6.      Ouellet J and Perreault JP.  Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate. RNA. 10 (7):1059-72 (2004) .  

7.       Wilson TJ, Ouellet J, Zhao ZY, Harusawa S, Araki L, Kurihara T and Lilley DM.    Nucleobase catalysis in hairpin riobozyme.  RNA. 12(6):980-7 (2006) .  

8.      Reymond C, Ouellet J, Bisaillon M and Perreault JP.  Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interaction of the L3 loop.  RNA. 13(1): 44-54 (2007) .  

9.      Lipfert J^#, Ouellet J^#, Norman DG, Doniach S and Lilley DM.  The complete VS ribozyme in solution studied by small-angle X-ray scattering. ^# These authors have an equal contribution.  Structure. 16(9):1357-67 (2008)

10.     Ouellet J, Byrne M and Lilley DM.  Formation of an active site in trans by interaction of two complete Varkud Satellite ribozymes. RNA. 15(10):1822-6 (2009) .  

11.     Schroeder KT, McPhee SA, Ouellet J and Lilley DM.  A structural database for k-turn motifs in RNA.  RNA. 16(8):1463-8 (2010) .  

12.     Ouellet J, Melcher S, Iqbal A, Ding Y and Lilley DM.  Structure of the three-way helical junction of the hepatitis C virus IRES element.  RNA. 16(8):1597-609 (2010) .  

13.     Ouellet J, Schorr S, Iqbal A, Wilson TJ, and Lilley DM.  Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers.  Biophysical Journal. 101(5):1148-54 (2011) .  

14.     Wang J, Fessl T, Schroeder KT, Ouellet J, Liu Y, Freeman ADJ and Lilley DM.  Single-molecule observation of the induced fit of k-turn RNA structure on binding L7Ae protein.  Biophysical Journal. 103(12):2541-8 (2012).  

15.     Ouellet J, Ananvoranich S and Perreault JP.  Structural Analysis of Ribozymes.  Encyclopedia of Analytical Chemistry.In the Press, 2013.

16.     Korbi AE, Ouellet J, Naghdi MR and Perreault J.  Finding Instances of Riboswitches and Ribozymes by Homology Search of Structured RNA with Infernal.  Methods in Molecular Biology.Accepted, 2013.

Presentations/Invited Talks

Posters

1. Research Day of the University of Sherbrooke. Structural Studies of the Peach Latent Mosaic Viroid. Jonathan Ouellet and Jean-Pierre Perreault. (2000)

2. 29^th Edition of the Scientific Day from the Faculty of Medicine of the University of Sherbrooke. A highly branched RNA. Jonathan Ouellet, Martin Pelchat, Fabien Côté, Dominique Lévesque and Jean-Pierre Perreault. (2000)

3. RNA Structure (Santa Cruz, California). Magnesium Binding Site and Rearrangements of the Delta Antigenomic Ribozyme. Jonathan Ouellet, Daniel A. Lafontaine, Sirinart Ananvoranich and Jean-Pierre Perreault. (2000)The number of participants was limited

4. Research Day 2001 of the University of Sherbrooke. Structural Studies of the Delta Ribozyme by Biochemical Analyses. Jonathan Ouellet and Jean-Pierre Perreault. (2001)

5. 6^th Annual Meeting of the RNA Society (Banff, Alberta). Structural Rearrangement and Magnesium Binding Site in the Delta Antigenomic Trans-Acting Ribozyme. Jonathan Ouellet and Jean-Pierre Perreault. (2001)

6. Opening 2001 of Eastern Riboclub (Magog, Québec). Rearrangement of the P2 Stem is an Essential Step in the Folding Pathway of Delta Ribozyme. Jonathan Ouellet and Jean-Pierre Perreault. (2001)

7. 7^th Annual Meeting of the RNA Society (Madison, Wisconsin). Real-Time Interaction Between a Trans-Acting Delta Ribozyme and its Substrate.Jonathan Ouellet and Jean-Pierre Perreault. (2002)

8. Ribozyme and RNA Catalysis/EMBO Workshop (Dundee, United Kingdom). Magnesium dependent crosslink of the delta ribozyme using an 4-thiouridine. Jonathan Ouellet and Jean-Pierre Perreault. (2002)

9. Opening 2002 of Eastern Riboclub (Magog, Québec). Mg⁺⁺ dependent crosslink in the antigenomic trans delta ribozyme using 4-thiouridine. Jonathan Ouellet and Jean-Pierre Perreault. (2002)

10. Opening 2003 of Eastern Riboclub (Magog, Québec). A Mg⁺⁺ dependent crosslink to monitor the folding pathway in the antigenomic trans delta ribozyme. Jonathan Ouellet and Jean-Pierre Perreault. (2003)

11. 9^th Annual Meeting of the RNA Society (Madison, Wisconsin). 4-thiouridine crosslinking revealed tertiary interaction between the substrate and the trans-acting antigenomic delta ribozyme core. Jonathan Ouellet and Jean-Pierre Perreault. (2004)

12. Opening 2004 of Eastern Riboclub (Magog, Québec). 4-thiouridine cross-linking to reveal the folding pathway of the antigenomic trans-acting delta ribozyme. Jonathan Ouellet and Jean-Pierre Perreault. (2003)

13. Nanobio summer school (Cargèse, Corse). Folding dynamics of the VS ribozyme. Jonathan Ouellet, Carlos Penedo and David M.J. Lilley. (2006)

14. Frontiers in Chemical Biology: Single Molecules (Cambridge, UK). Single molecule folding of the VS ribozyme. Jonathan Ouellet, Carlos Penedo and David M.J. Lilley. (2006)

15. 13^th Annual Meeting of the RiboClub (Magog, Québec). The Varkud Satellite Ribozyme : Structure and Mechanism. Jonathan Ouellet, Jan Lipfert, David G. Norman, Carlos Penedo and David M.J. Lilley. (2012)

Invited Speaker

1. Eastern Riboclub Opening 2004 at the Hotel Cheribourg from Magog. 3D Graphical Animation of the Complete Delta Ribozyme Folding Pathway. (2004) Invited by D^r S. Abou Elela

2. Chemistry Club Lecture Series at Monmouth University. RNA Structure: From Aptamer Selection to Curing Diseases. (2013) Invited by the chemistry club’s president Patrick Fedick.

Speaker

1. 68^th Congress of ACFAS at the University of Montreal. Structural Studies of the Peach Latent Mosaic Viroid. (2000)

2. 8^th Scientific Symposium in Biochemistry of the University of Sherbrooke. Real-Time Tertiary Interactions Between the HDV Ribozyme and its Trans Substrates. (2002)

3. Eastern Riboclub at the University of Sherbrooke. Crosslink with 4-Thiouridine in the Antigenomic Trans Delta Ribozyme. (2002)

4. 9^th Scientific Symposium in Biochemistry of the University of Sherbrooke. Folding Dynamics of the HDV Ribozyme and its Trans Substrate by Crosslinking. (2003)

5. 10^th Scientific Symposium in Biochemistry of the University of Sherbrooke. Folding Dynamics of the HDV Ribozyme and its Trans Substrate by Crosslinking. (2004)

6. 13^th Annual Meeting of the RNA Society in Berlin, Germany; plenary session. New insights into an RNA enzyme. (2008)

7. Dundee’s CLSPA (College of Life Sciences Post-Doc Association) at the University of Dundee, UK. New insights of an RNA enzyme. (2008)

8. The Nucleic Acids Forum 2010 at the University of Liverpool, UK. Structure and dynamics of an RNA helical junction in the hepatitis C virus IRES element. (2010)

9. 96^th Canadian Chemistry Conference and Exhibition 2013 at the Centre des congrès de Québec. An innovative strategy for the selection of aptamers based on native PAGE slabs: SR-PAGE. (2013