Carlos Penedo Esteiro

Carlos Penedo

Postal address:
School of Physics & Astronomy
Physical Science Building
North Haugh
St Andrews
United Kingdom


Web address:

Direct phone: +44 (0)1334 463106

Research overview

We are interested in the use and development of novel biophysical techniques to study biomolecular interactions including proteins, DNA and RNA at the level of individual molecules. The advantages of single-molecule detection are many, apart from the fascination of looking at individual biomolecules at work, single-molecule techniques can measure intermediates and follow time-dependent pathways of chemical reactions and folding mechanisms that are difficult or impossible to synchronize at the ensemble level. Thus, single-molecule techniques provide novel insights into how molecules and systems behave, having the advantage that spatial and temporal averaging is avoided, temporal synchronisation is not necessary and novel phenomena, which otherwise are averaged and remain hidden in ensembles, may be discovered. Our aim is to monitor, in real-time, the behaviour of individual biological molecules and complexes, in vitro and in live cells. By combining the dynamic information obtained at the single-molecule or single-complex level with structural and biochemical analyses, we hope to create “molecular movies” of biological processes and from them obtain a deeper understanding of these processes.

Recent Publications

Real-time conformational switching of single conjugated polymer chains in solution
Tenopala Carmona, F., Fronk, S., Bazan, G. C., Samuel, I. D. W. & Penedo-Esteiro, J. C. 16 Feb 2018 In : Science Advances. 4, 2, 13 p., eaao5786
Research output: Research - peer-reviewArticle

DNA binding and unwinding by Hel308 helicase requires dual functions of a winged helix domain
Northall, S. J., Buckley, R., Jones, N., Penedo-Esteiro, J. C., Soultanas, P. & Bolt, E. Sep 2017 In : DNA Repair. 57, p. 125-132 7 p.
Research output: Research - peer-reviewArticle

Transcriptional dynamics
Lafontaine, D. A. & Penedo-Esteiro, J. C. 1 May 2017 In : Methods. 120, p. 1-2 2 p.
Research output: Research - peer-reviewEditorial

High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein
Morten, M. J., Gamsjaeger, R., Cubeddu, L., Kariawasam, R., Peregrina, J. R., Penedo-Esteiro, J. C. & White, M. F. Mar 2017 In : Extremophiles. 21, 2, p. 369-379 11 p.
Research output: Research - peer-reviewArticle

Morphology-specific inhibition of β-amyloid aggregates by 17β-hydroxysteroid dehydrogenase type 10
Aitken, L., Quinn, S. D., Perez-Gonzalez, D. C., Samuel, I. D. W., Penedo-Esteiro, J. C. & Gunn-Moore, F. J. 2 Jun 2016 In : ChemBioChem. 17, 11, p. 1029-1037
Research output: Research - peer-reviewArticle

Biophysical approaches to gene regulation by riboswitches: Biophysics of Infection
Perez Gonzalez, D. C., Grondin, J. P., Lafontaine, D. A. & Penedo-Esteiro, J. C. 19 May 2016 Advances in Experimental Medicine and Biology: Biophysics of Infection. Leake, M. C. (ed.). Switzerland: Springer, Vol. 915, p. 157-190
Research output: ResearchChapter

Mechanism of DNA loading by the DNA repair helicase XPD
Constantinescu-Aruxandei, D., Petrovic-Stojanovska, B., Penedo, C., White, M. F. & Naismith, J. H. 7 Apr 2016 In : Nucleic Acids Research. 44, 6, p. 2806-2815 10 p.
Research output: Research - peer-reviewArticle

Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach
Morten, M. J., Peregrina, J. R., Figueira-Gonzalez, M., Ackermann, K., Bode, B. E., White, M. F. & Penedo, C. 15 Dec 2015 In : Nucleic Acids Research. 43, 22, p. 10907-10924
Research output: Research - peer-reviewArticle

Single-molecule approaches for the characterization of riboswitch folding mechanisms
Penedo, C., Boudreault, J., Perez Gonzalez, D. C. & Lafontaine, D. A. 1 Oct 2015 In : Methods in molecular biology (Clifton, N.J.). 1334, p. 101-107
Research output: Research - peer-reviewArticle

Functional studies of DNA-protein interactions using FRET techniques
Blouin, S., Craggs, T. D., Lafontaine, D. A. & Penedo, C. 1 Oct 2015 In : Methods in Molecular Biology. 1334, p. 115-141
Research output: Research - peer-reviewArticle

RNA and DNA Diagnostics: Single-Molecule Strategies for DNA and RNA Diagnostics
Perez Gonzalez, D. C. & Penedo, C. 15 Jun 2015 RNA technologies. Erdmann, V. A., Jurga, S. & Barciszewski, J. (eds.). Springer, p. 297-332
Research output: ResearchChapter

Towards ratiometric sensing of amyloid fibrils in vitro
Freire, S., Rodriguez-Prieto, F., Rios-Rodriguez, M. C., Penedo, C., Al-Soufi, W. & Novo, M. 16 Feb 2015 In : Chemistry - A European Journal. 21, 8, p. 3425-3434
Research output: Research - peer-reviewArticle

The phosphorylation of Hsp20 enhances its association with amyloid-β to increase protection against neuronal cell death
Cameron, R. T., Quinn, S. D., Cairns, L. S., MacLeod, R., Samuel, I. D. W., Smith, B. O., Penedo, C. & Baillie, G. S. Jul 2014 In : Molecular and Cellular Neuroscience. 61, p. 46-55 10 p.
Research output: Research - peer-reviewArticle

Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates
Craggs, T. D., Brenlla, A., Hutton, R. D., White, M. F. & Penedo, C. Feb 2014 In : Nucleic Acids Research. 42, 3, p. 1857-1872
Research output: Research - peer-reviewArticle

Real-time probing of β-amyloid self-assembly and inhibition using fluorescence self-quenching between neighbouring dyes
Quinn, S. D., Dalgarno, P. A., Cameron, R. T., Hedley, G. J., Hacker, C., Lucocq, J. M., Samuel, I. D. W. & Penedo, C. Jan 2014 In : Molecular BioSystems. 10, 1, p. 34-44 11 p.
Research output: Research - peer-reviewArticle

Single-molecule chemical denaturation of riboswitches
Dalgarno, P. A., Bordello, J., Morris, R., St-Pierre, P., Dubé, A., Samuel, I. D. W., Lafontaine, D. & Penedo, C. Feb 2013 In : Nucleic Acids Research. 41, 7, p. 4253-4265
Research output: Research - peer-reviewArticle

Solution-Based Single Molecule Imaging of Surface-Immobilized Conjugated Polymers
Dalgarno, P. A., Traina, C. A., Penedo, C., Bazan, G. & Samuel, I. D. W. 2013 In : Journal of the American Chemical Society. 135, 19, 7187-7193
Research output: Research - peer-reviewArticle

Single molecule Fluorescence of Nucleic Acids
McCluskey, K., Shaw, E. S., Lafontaine, D. & Penedo, C. 2013 (Accepted/In press) Methods in Molecular Biology: Fluorescence microscopy and spectroscopy. Vol. 1076
Research output: ResearchChapter

Constitutive Regulatory Activity of an Evolutionarily Excluded Riboswitch Variant
Tremblay, R., Lemay, J-F., Blouin, S., Mulhbacher, J., Bonneau, E., Legault, P., Dupont, P., Penedo, C. & Lafontaine, D. A. 5 Aug 2011 In : Journal of Biological Chemistry. 286, 31, p. 27406-27415 10 p.
Research output: Research - peer-reviewArticle

Molecular insights into the ligand-controlled organization of SAM-I riboswitch
Heppell, B., Blouin, S., Dussault, A. M., Muhlbacher, J., Ennifar, J., Penedo, C. & Lafontaine, D. Jun 2011 In : Nature Chemical Biology. 7, 6, p. 384-392
Research output: Research - peer-reviewArticle

PCNA and XPF cooperate to distort DNA substrates
Hutton, R. D., Craggs, T. D., White, M. F. & Penedo, C. Mar 2010 In : Nucleic Acids Research. 38, 5, p. 1664-1675 12 p.
Research output: Research - peer-reviewArticle

Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches
Penedo-Esteiro, J. C., Lemay, J. F., Mulbacher, J. & Lafontaine, D. 2009 Methods in Molecular Biology. Serganov, A. (ed.). New Jersey: Humana Press, Vol. 540
Research output: ResearchChapter

Functional studies of DNA-protein interactions using FRET techniques
Penedo-Esteiro, J. C., Blouin, S. & Lafontaine, D. 2009 Methods in Molecular Biology. Moss, T. & Leblanc, B. (eds.). New Jersey: Humana Press, Vol. 543
Research output: ResearchChapter

Application of fluorescence measurements for characterization of riboswitch-ligand interactions
Penedo-Esteiro, J. C., Heppell, B., Mulbacher, J. & Lafontaine, D. 2009 Methods in Molecular Biology. New Jersey: Humana Press, Vol. 540
Research output: ResearchChapter

PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step
Hutton, R. D., Roberts, J. A., Penedo, C. & White, M. F. Dec 2008 In : Nucleic Acids Research. 36, 21, p. 6720-6727 8 p.
Research output: Research - peer-reviewArticle