Principal Investigator: Dr. Carlos Penedo

The lysine riboswitch regulates gene expression using a dual-layer control mechanism
K. McCluskey, J. Boudreault, P. St-Pierre, D. A. Lafontaine and J. Carlos Penedo. To be submitted

    2017  
The folding pathway of the adenine riboswitch involves a structural intermediate preorganizing the binding domain
P. St-Pierre, Samuel Jacques, C. Perez-Gonzalez, F. Picard-Jean, J.C. Penedo* and D.A. Lafontaine*. to be submitted

    2017  
Direct observation and conformational manipulation of single conjugated polymers in solution
F. Tenopala-Carmona, S. Fronk, G. Bazan, I. D. W. Samuel* and J. Carlos Penedo* Submitted

    2017  
Single-molecule FRET imaging of nascent RNA within transcription elongation complexes
A. Chauvier, P. St-Pierre, J.F. Nadon, J.P. Grondin, C. Perez-Gonzalez, S.H. Eschbach, A.M. Lamontagne, J.C. Penedo* and D.A. Lafontaine*. Submitted

    2017  
DNA binding and unwinding of forked DNA by Hel308 requires dual functions of a winged helix domain. Sarah J Northall, Ryan Buckey, Nathan Jones, J. Carlos Penedo, Panos Soultanas and Edward Bolt. DNA repair, 57, 125-132
    2017  
Transcriptional dynamics
Daniel A Lafontaine*, J. Carlos Penedo*. Editorial preface special topic in 'Transcriptional dynamics' Methods, Vol 120, 1-2
    2017  

An integrated perspective on RNA aptamer ligand recognition models: clearing muddy waters
Kaley McCluskey*, J. Carlos Penedo*. Phys. Chem. Chem. Phys. In press doi: 10.1039/C6CP08798A

    2017  
High affinity RNA binding by a hyperthermophilic single-stranded DNA binding protein
Michael Morten, Roland Gamsjaeger, Ruvini Kariawasam, Liza Cubeddu, Jose Peregrina, Elena Evgureieva-Hackenberg, J. Carlos Penedo and Malcolm F. White. Extremophiles. doi:10.1007/s00792-016-0910-2
    2016
 
Fluorescence-based strategies to investigate the structure and dynamics of RNA aptamer-ligand complexes
Cibran Perez-Gonzalez, Daniel A. Lafontaine*, J. Carlos Penedo* Frontiers in Chemistry, special topic in Natural and artificially-engineered nucleic acid aptamers: design, characterization and technological applications: Eds. Daniel A. Lafontaine and J. Carlos Penedo, Front. Chem. doi: 10.3389/fchem.2016.00033
    2016  
 
Morphology-specific inhibition of b-amyloid aggregates by 17b-hydroxysteroid dehydrogenase type 10
Laura Aitken, Steven D. Quinn, Daniel C. Perez-Gonzalez, Ifor D. W. Samuel, J. Carlos Penedo* and Frank Gunn-Moore* ChemBioChem. 17, 1029-1037.
    2016
 
Biophysical approaches to bacterial gene regulation by riboswitches
Cibran Perez-Gonzalez, Daniel A. Lafontaine* and J. Carlos Penedo* Advances in Experimental Medicine and Biology, 915, 157-191
    2016
 
Mechanism of DNA loading by the DNA repair helicase XPD
Diana Constantinescu Aruxandei, Biljana Petrovic-Stojanovska, J. Carlos Penedo, Malcolm F. White and James Naismith Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw102
    2016
 
Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach
Michael J. Morten, Jose R. Peregrina, Maria Figueira-Gonzalez, Katrin Ackermann, Bela E Bode, Malcolm F. White* and J. Carlos Penedo* Nucleic Acids Res. 43(22), 10907-10924
    2015
 
Functional Studies of DNA-Protein Interactions Using FRET Techniques
S Blouin, TD Craggs, DA Lafontaine, JC Penedo DNA-Protein Interactions, Methods in Molecular Biology, 115-141
2015
 
Single-molecule approaches for the characterization of riboswitch folding mechanisms
Julien Boudreault, D. Cibran Perez-Gonzalez, J. Carlos Penedo and Daniel A. Lafontaine. DNA-Protein interactions: Methods and Protocols. Methods Mol. Biol. Vol 1334, 115-141
2015
 
Single-molecule strategies for DNA and RNA diagnostics
D. Cibran Perez-Gonzalez, J. Carlos Penedo, RNA Technologies:
RNA and DNA diagnostics. Springer-Verlag. Eds (D. A. Erdmann, S. Jurga and J. Barciszweski) pp 297-332
2015
 
Towards ratiometric sensing of amyloid fibrils in vitro
Sonia Freire, Flor Rodriguez-Prieto, M. Carmen Rios Rodriguez, J. Carlos Penedo, Wajih Al-Soufi and Mercedes Novo*,
Chemistry- A European Journal, 21, 3425 – 3434
2015
 
Using smFRET and denaturants to reveal folding landscapes
E. Shaw, K. McCluskey, P. St-Pierre, Daniel A. Lafontaine* and J. Carlos Penedo* Methods in Enzymology. Vol. 549, 313-341
2014
 
 
Phosphorylation of Hsp20 enhances its association with beta-amyloid to increase protection against neuronal cell death
Ryan T. Cameron, Steven D. Quinn, Lynn S. Z. Cairns, Ruth MacLeod, Brian O. Smith,Ifor D. W. Samuel, J. Carlos Penedo and George S. Baillie.Molecular and Cellular Neurosciences. In press .DOI: 1016/j.mcn.2014.05.002
2014
 
 
Fluorescence tools to investigate riboswitch structural dynamics
P. St-Pierre, K. McCluskey, E. Shaw, J. Carlos Penedo* and Daniel A Lafontaine*.BBA-Gene regulatory Mechanisms. In press. DOI: 10.1016/j.bbagrm.2014.05.015
2014
 
 
Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates
Timothy D. Craggs, Richard D. Hutton, Alfonso Brenlla, Malcolm F. White and J. Carlos Penedo, Nucleic Acids Res. doi: 10.1093/nar/gkt1116
2014

 

 

Single-Molecule Fluorescence of Nucleic Acids
K McCluskey, E Shaw, DA Lafontaine, JC Penedo
Fluorescence Spectroscopy and Microscopy, Methods in Molecular Biology,1076 759-791
2013
Real-time probing of amyloid aggreation and inhibition using fluorescence self-quenching between neighbouring dyes
SD Quinn, PA Dalgarno, RT Cameron, GJ Hedley, C Hacker, JM Lucocq, GS Baillie, IDW Samuel, JC Penedo.Mol. BioSyst., 2014, 10 (1), 34 - 44

  2013
 
Solution-Based Single Molecule Imaging of Surface-Immobilized Conjugated Polymers
PA Dalgarno, CA Traina, JC Penedo, GC Bazan, IDW Samuel
Journal of the American Chemical Society
2013
 
 
Single-molecule chemical denaturation of riboswitches
PA Dalgarno, J Bordello, R Morris, P St-Pierre, A Dubé, IDW Samuel, DA, Daniel A. Lafontaine and J. Carlos Penedo Nucleic acids research
2013
 
Folding of the SAM-I riboswitch: A tale with a twist
SH Eschbach, P St-Pierre, JC Penedo, DA Lafontaine
RNA Biology 9 (5), 535-541
2012
Constitutive regulatory activity of an evolutionarily excluded riboswitch variant
R Tremblay, JF Lemay, S Blouin, J Mulhbacher, É Bonneau, P Legault, P Dupont ...
Journal of Biological Chemistry 286 (31), 27406-27415
2011
 
   
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch
B Heppell, S Blouin, AM Dussault, J Mulhbacher, E Ennifar, JC Penedo, DA ...
Nature Chemical Biology 7 (6), 384-392
  2011
 
 
PCNA and XPF cooperate to distort DNA substrates
RD Hutton, TD Craggs, MF White, JC Penedo
Nucleic acids research 38 (5), 1664-1675
2010
 
Riboswitches: ancient and promising genetic regulators
S Blouin, J Mulhbacher, JC Penedo, DA Lafontaine
Chembiochem 10 (3), 400-416
2009
 
Natural Functional Nucleic Acids: Ribozymes and Riboswitches
R Tremblay, J Mulhbacher, S Blouin, JC Penedo, DA Lafontaine
Functional Nucleic Acids for Analytical Applications, 11-46
2009
 
Functional Studies of DNA-Protein Interactions Using FRET Techniques
S Blouin, TD Craggs, DA Lafontaine, JC Penedo
DNA-Protein Interactions, Methods in Molecular Biology, 475-502
2009
 
Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches
JF Lemay, JC Penedo, J Mulhbacher, DA Lafontaine
Riboswitches, Methods in Molecular Biology, 65-76
2009
 
Application of fluorescent measurements for characterization of riboswitch–ligand interactions
B Heppell, J Mulhbacher, JC Penedo, DA Lafontaine
Riboswitches, Methods in Molecular Biology,25-37
2009
PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step
RD Hutton, JA Roberts, JC Penedo, MF White
Nucleic acids research 36 (21), 6720-6727
2008
Solvent dependent photophysics of fac-[Re (CO) 3 (11, 12-X2dppz)(py)]+(X= H, F or Me)
J Dyer, CM Creely, JC Penedo, DC Grills, S Hudson, P Matousek, AW Parker, M
Photochemical & Photobiological Sciences 6 (7), 741-748
2007
Folding of the adenine riboswitch
JF Lemay, JC Penedo, R Tremblay, DMJ Lilley, DA Lafontaine
Chemistry & Biology 13 (8), 857-868
2006
 
Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: dissociative mechanism versus water-assisted proton transfer
JC Penedo, MC Ríos Rodríguez, I García Lema, JL Pérez Lustres, M Mosquera, F ...
The Journal of Physical Chemistry A 109 (45), 10189-10198
2005
 
Photophysical study of a family of [Ru (phen) 2 (Mendpq)] 2+ complexes in different solvents and DNA: a specific water effect promoted by methyl substitution
K O'Donoghue, JC Penedo, JM Kelly, PE Kruger
Dalton Transactions, 1123-1128
2005
Solvent-dependent ground-and excited-state tautomerism in 2-(6'-hydroxy-2'-pyridyl) benzimidazole
JC Penedo, JLP Lustres, IG Lema, MCR Rodríguez, M Mosquera, F Rodríguez-Prieto
The Journal of Physical Chemistry A 108 (29), 6117-6126
2004
 
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
JC PENEDO, TJ WILSON, SD JAYASENA, A KHVOROVA, DMJ LILLEY
RNA 10 (5), 880-888
2004
Ultrafast transient absorption studies of ruthenium and rhenium dipyridophenazine complexes bound to DNA and polynucleotides
CM Creely, JM Kelly, MM Feeney, S Hudson, JC Penedo, WJ Blau, B Elias, A ...
OPTO Ireland, Proceedings SPIE, 92-102
2003
Role of hydrogen-bonded adducts in excited-state proton-transfer processes
JC Penedo, M Mosquera, F Rodríguez-Prieto
The Journal of Physical Chemistry A 104 (32), 7429-7441
2000
On the Mechanism of Alcohol-Catalyzed Excited-State Intramolecular Proton Transfer in Cationic Benzimidazoles
MCR Rodríguez, JC Penedo, RJ Willemse, M Mosquera, F Rodríguez-Prieto
The Journal of Physical Chemistry A 103 (36), 7236-7243
1999
Solvent control of molecular structure and excited-state proton-transfer processes of 1-methyl-2-(2′-hydroxyphenyl)-benzimidazole
F Rodríguez-Prieto, JC Penedo, M Mosquera
Journal of the Chemical Society, Faraday Transactions 94 (18), 2775-2782
1998
Photoinduced Inter-and Intramolecular Proton Transfer in Aqueous and Ethanolic Solutions of 2-(2'-Hydroxyphenyl) benzimidazole: Evidence for Tautomeric and Conformational Equilibria in the Ground State
M Mosquera, JC Penedo, MC Ríos Rodríguez, F Rodríguez-Prieto
The Journal of Physical Chemistry 100 (13), 5398-5407
1996