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

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

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

Asymmetric base pair opening drives helicase unwinding dynamics
Francesco Colizzi, Cibran Perez-Gonzalez, Yaakov Levy, Malcolm F. White, J. Carlos Penedo* and Giovanni Bussi*. To be submitted

Real-time observation of conformational switching in single conjugated polymers chains.
F. Tenopala-Carmona, S. Fronk, G. Bazan*, I. D. W. Samuel* and J. Carlos Penedo* Science Advances, Vol. 4, no. 2, eaao5786

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
Transcriptional dynamics
Daniel A Lafontaine*, J. Carlos Penedo*. Editorial preface special topic in 'Transcriptional dynamics' Methods, Vol 120, 1-2

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

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
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
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.
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
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
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
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
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
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
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
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
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
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
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



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
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

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
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
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
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
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
PCNA and XPF cooperate to distort DNA substrates
RD Hutton, TD Craggs, MF White, JC Penedo
Nucleic acids research 38 (5), 1664-1675
Riboswitches: ancient and promising genetic regulators
S Blouin, J Mulhbacher, JC Penedo, DA Lafontaine
Chembiochem 10 (3), 400-416
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
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
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
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
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
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
Folding of the adenine riboswitch
JF Lemay, JC Penedo, R Tremblay, DMJ Lilley, DA Lafontaine
Chemistry & Biology 13 (8), 857-868
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
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
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
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
RNA 10 (5), 880-888
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
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
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
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
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