Principal Investigator: Dr. Carlos Penedo

Laboratory for Biophysics and Biomolecular Dynamics

 

Publications

 

Solution-based single-molecule imaging of surface-immobilized conjugated polymers

  • Single-molecule chemical denaturation of riboswitches

  • DOI: 10.1093/nar/gkt128
  • Nucleic Acids Res. 2013 41(7):4253-65 (Featured Article)

  • Folding of the SAM-I riboswitch: A tale with a twist

    DOI: 10.4161/rna
  • Eschbach, S.H. and St-Pierre, P. and Penedo, J.C. and Lafontaine, D.A., (2012). RNA Biology, vol. 9, no. 5, pp. 535-541

  • Single-molecule fluorescence studies of nucleic acids

  • DOI: 10.4161/rna
  • Eschbach, S.H. and St-Pierre, P. and Penedo, J.C. and Lafontaine, D.A., (2012). RNA Biology, vol. 9, no. 5, pp. 535-541

Constitutive regulatory activity of an evolutionarily excluded riboswitch variant

DOI: 10.1074/jbc.M111.229047

Tremblay, R. and Lemay, J.-F. and Blouin, S. and Mulhbacher, J. and Bonneau, É. and Legault, P. and Dupont, P. and Penedo, J.C. and Lafontaine, D.A., Journal of Biological Chemistry, 2011 vol. 286, no. 31, pp. 27406-27415

Molecular insights into the ligand-controlled organization of the SAM-I riboswitch

DOI: 10.1038/nchembio.563

Heppell, B. and Blouin, S. and Dussault, A.-M. and Mulhbacher, J. and Ennifar, E. and Penedo, J.C. and Lafontaine, D.A. Nature Chemical Biology, 2011 vol. 7, no. 6, pp. 384-392

Application of fluorescent measurements for characterization of riboswitch-ligand interactions.

DOI: 10.1007/978-1-59745-558-9_3

Heppell, B. and Mulhbacher, J. and Penedo, J.C. and Lafontaine, D.A., (2009). Methods in molecular biology (Clifton, N.J.), vol. 540, pp. 25-37

  • Functional studies of DNA-protein interactions using FRET techniques

    DOI: 10.1007/978-1-60327-015-1_28
  • Blouin, S. and Craggs, T.D. and Lafontaine, D.A. and Penedo, J.C., (2009). Methods in Molecular Biology, vol. 543, pp. 475-502

Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches.

DOI: 10.1007/978-1-59745-558-9_6

Lemay, J.F. and Penedo, J.C. and Mulhbacher, J. and Lafontaine, D.A., (2009). Methods in molecular biology (Clifton, N.J.), vol. 540, pp. 65-76

  • PCNA and XPF cooperate to distort DNA substrates

    DOI: 10.1093/nar/gkp1104
  • Hutton, R.D. and Craggs, T.D. and White, M.F. and Penedo, J.C., (2009). Nucleic Acids Research, vol. 38, no. 5, pp. 1664-1675

  • Riboswitches: Ancient and promising genetic regulators

    DOI: 10.1002/cbic.200800593
  • Blouin, S. and Mulhbacher, J. and Penedo, J.C. and Lafontaine, D.A., (2009). ChemBioChem, vol. 10, no. 3, pp. 400-416

PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: Substrate targeting and catalytic step

  • DOI: 10.1093/nar/gkn745
  • Hutton, R.D. and Roberts, J.A. and Penedo, J.C. and White, M.F., (2008). Nucleic Acids Research, vol. 36, no. 21, pp. 6720-6727

Solvent dependent photophysics of fac-[Re(CO)3(11,12-X 2dppz)(py)]+ (X = H, F or Me)

  • DOI: 10.1039/b618651c
  • Dyer, J. and Creely, C.M. and Penedo, J.C. and Grills, D.C. and Hudson, S. and Matousek, P. and Parker, A.W. and Towrie, M. and Kelly, J.M. and George, M.W., (2007). Photochemical and Photobiological Sciences, vol. 6, no. 7, pp. 741-748

Folding of the Adenine Riboswitch

  • DOI: 10.1016/j.chembiol.2006.06.010
  • Lemay, J.-F. and Penedo, J.C. and Tremblay, R. and Lilley, D.M.J. and Lafontaine, DanielA., (2006). Chemistry and Biology, vol. 13, no. 8, pp. 857-868

Photophysical study of a family of [Ru(phen)2(Me ndpq)]2+ complexes in different solvents and DNA: A specific water effect promoted by methyl substitution

  • DOI: 10.1039/b418362b
  • 'O'Donoghue, K. and Penedo, J.C. and Kelly, J.M. and Kruger, P.E., (2005). Dalton Transactions, no. 6, pp. 1123-1128

Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: Dissociative mechanism versus water-assisted proton transfer

  • DOI: 10.1021/jp0518355
  • Penedo, J.C. and Ríos Rodríguez, M.C. and Lema, I.G. and Lustres, J.L.P. and Mosquera, M. and Rodríguez-Prieto, F., (2005). Journal of Physical Chemistry A, vol. 109, no. 45, pp. 10189-10198

Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

  • DOI: 10.1261/rna.5268404
  • Penedo, J.C. and Wilson, T.J. and Jayasena, S.D. and Khvorova, A. and Lilley, D.M.J., (2004). RNA, vol. 10, no. 5, pp. 880-888

Solvent-dependent ground- and excited-state tautomerism in 2-(6′-hydroxy-2′-pyridyl)benzimidazole

  • DOI: 10.1021/jp049056w
  • Penedo, J.C. and Lustres, J.L.P. and Lema, I.G. and Rodríguez, M.C.R. and Mosquera, M. and Rodríguez-Prieto, F., (2004). Journal of Physical Chemistry A, vol. 108, no. 29, pp. 6117-6126

Ultrafast transient absorption studies of ruthenium and rhenium dipyridophenazine complexes bound to DNA and polynucleotides

  • DOI: 10.1117/12.463625
  • Creely, C.M. and Kelly, J.M. and Feeney, M.M. and Hudson, S. and Penedo, J.C. and Blau, W.J. and Elias, B. and Kirsch-De Mesmaeker, A. and Matousek, P. and Towrie, M. and Parker, A.W. and Dyer, J.S. and George, M.W. and Coates, C.G. and Mc Garvey, J.J., (2002). Proceedings of SPIE - The International Society for Optical Engineering, vol. 4876, no. 1, pp. 92-102

  • Role of hydrogen-bonded adducts in excited-state proton-transfer processes

  • http://www.scopus.com/inward/record.url?eid=2-s2.0-0034247495&partnerID=MN8TOARS
  • Penedo, J.C. and Mosquera, M. and Rodríguez-Prieto, F., (2000). Journal of Physical Chemistry A, vol. 104, no. 32, pp. 7429-7441

  • On the Mechanism of Alcohol-Catalyzed Excited-State Intramolecular Proton Transfer in Cationic Benzimidazoles: Journal of Physical Chemistry A 1999

  • http://www.scopus.com/inward/record.url?eid=2-s2.0-0001380254&partnerID=MN8TOARS
  • Ríos Rodríguez, M.C. and Penedo, J.C. and Willemse, R.J. and Mosquera, M. and Rodríguez-Prieto, F., (1999). Journal of Physical Chemistry A, vol. 103, no. 36, pp. 7236-7243

  • Solvent control of molecular structure and excited-state proton-transfer processes of 1-methyl-2-(2′-hydroxyphenyl)-benzimidazole: Journal of the Chemical Society - Faraday Transactions 1998

    Rodríguez-Prieto, F. and Penedo, J.C. and Mosquera, M., (1998). Journal of the Chemical Society - Faraday Transactions, vol. 94, no. 18, pp. 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: Journal of Physical Chemistry 1996

    Mosquera, M. and Penedo, J.C. and Ríos Rodríguez, M.C. and Rodrìguez-Prieto, F., (1996). Journal of Physical Chemistry, vol. 100, no. 13, pp. 5398-5407