Publications
2023
Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB
2022
Optical Tweezers to Force Information out of Biological and Synthetic Systems One Molecule at a Time.
Bocanegra, R.; Ortiz-Rodríguez, M.; Garcia-Abadillo, I.P.; R-Pulido, C.; Ibarra, B.
2021
Cooperative-dependent folding of single-stranded DNA
Viader-Godoy, C. R. Pulido, B. Ibarra, M. Manosas, F. Ritort.
Physical Review X; 11, 031037 (2021).
DNA replication machinery: Insights from in vitro single-molecule approaches
, Ismael Plaza G.A., Carlos R. Pulido,
Computational and Structural Biotechnology Journal Vol 19, 2057-69, 2021
GTP and lipids control self-assembly and functional promiscuity of Dynamin2 molecular machinery
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Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins
Fernando Cerrón,
Methods in Molecular Biology, vol. 2281, Springer Nature 2021
DNA replication: In vitro single-molecule manipulation data analysis and models
Computational and Structural Biotechnology Journal, 19, 3765-3778 (2021).
In vitro single-molecule manipulation studies of viral DNA replication
Bocanegra R, Plaza G-A I, Ibarra B
The Enzymes. 2021;49:115-148.
Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-Binding Protein-DNA Complexes.
Methods in Molecular Biology, vol 2281 (2021)
Morin J.A., Cerrón F., Cao-García F.J., Ibarra B.
2020
Five Minutes in the Life of a Molecular Shuttle: Near-Equilibrium Measurements of Shuttling Dynamics Using Optical Tweezers.
Lemishko K.M., Naranjo T., Pérez E.M., Ibarra B.
Building and Probing Small for Mechanics. Advances in Atom and Single Molecule Machines. Springer, Cham. vol 2281 (2021).
2020
Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes
Nucleic Acids Research April 2020.
2019
Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis
F. Cerron, S. de Lorenzo, K.M. Lemishko, G. Ciesielski, L.S. Kaguni, F. Cao, B. Ibarra.
Nucleic Acids Research 2019, Vol 47, 11, 5723–5734,
2019
Dynamic constriction and fission of ER membranes by reticulon
J. Espadas, D. Pendin, R. Bocanegra, A. Escalada, G. Misticoni, T. Trevisan, A. Velasco del Olmo, S. Bova, B. Ibarra, P. I. Kuzmin, A.V. Shnyrova, V. A. Frolov, A. Daga
Nature Communications 10, 5327 (2019)
2018
Dynamics of individual molecular shuttles under mechanical force
Teresa Naranjo, Kateryna M. Lemishko, Sara de Lorenzo, Álvaro Somoza, Felix Ritort, Emilio M. Pérez & Borja Ibarra
Nature Communications volume 9, Article number: 4512 (2018)
2017
Mechanical measurement of hydrogen bonded host-guest systems under non-equilibrium, near-physiological conditions
Naranjo T, Cerrón F, Nieto-Ortega B, Latorre A, Somoza Á, Ibarra B*, Pérez EM*. *corresponding authors
Chemical Science 2017 Sep 1; 8(9): 6037–6041.
2017
DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein
Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B.
Nucleic Acids Research 2017 Jul 7;45(12):7237-7248.
2017
Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers
J Jarillo, JA Morín, E Beltrán-Heredia, JP Villaluenga, B Ibarra , FJ Cao.
PLoS One. 2017 Apr 5;12(4):e0174830
2016
Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments
José A Morin, Borja Ibarra and Francisco J Cao.
Journal of Statistical Mechanics: Theory and Experiment, Volume 2016, May 2016
2017
Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers
Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JP, Ibarra B, Cao FJ.
PLoS One. 2017 Apr 5;12(4):e0174830
2016
Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments
José A Morin, Borja Ibarra and Francisco J Cao.
Journal of Statistical Mechanics: Theory and Experiment, Volume 2016, May 2016
2015
Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase
J.A. Morin, F.J. Cao, J.M. Lázaro, J.R. Arias-Gonzalez, J.M. Valpuesta, J.L. Carrascosa, M. Salas, B. Ibarra
Nucleic Acids Research, 2015 Apr 20;43(7):3643-52.
2012
Manipulation of single polymerase-DNA complexes: a mechanical view of DNA unwinding during replication
Morin J.A., Cao F.J., Valpuesta J.M., Carrascosa J.L., Salas M., Ibarra B.
Cell Cycle 2016, 11(16): 2967- 2968
2015
Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase
J.A. Morin, F.J. Cao, J.M. Lázaro, J.R. Arias-Gonzalez, J.M. Valpuesta, J.L. Carrascosa, M. Salas, B. Ibarra
Nucleic Acids Res. 2015 Apr 20;43(7):3643-52.
2012
Manipulation of single polymerase-DNA complexes: a mechanical view of DNA unwinding during replication
Morin J.A., Cao F.J., Valpuesta J.M., Carrascosa J.L., Salas M., Ibarra B.
Cell Cycle 11(16): 2967- 2968
2012
Active DNA unwinding dynamics during processive DNA replication
J.A. Morin, F.J. Cao, J.M. Lázaro, J.R. Arias-Gonzalez, J.M. Valpuesta, J.L. Carrascosa, M. Salas, B. Ibarra
Proceedings of the National Academic of Sciences USA 109(21): 8115-20
2012
Mechanical stability of low-humidity single DNA molecules
Hormeño S., Ibarra B., Valpuesta J.M., Carrascosa J.L., Ricardo Arias-Gonzalez J.
Biopolymers, 97(4): 199-208
2012
Active DNA unwinding dynamics during processive DNA replication
J.A. Morin, F.J. Cao, J.M. Lázaro, J.R. Arias-Gonzalez, J.M. Valpuesta, J.L. Carrascosa, M. Salas, B. Ibarra
PNAS,2012,109(21): 8115-20
2012
Mechanical stability of low-humidity single DNA molecules
Hormeño S., Ibarra B., Valpuesta J.M., Carrascosa J.L., Ricardo Arias-Gonzalez J.
Biopolymers, 2012 97(4): 199-208
2011
Mechanical properties of high-GC content DNA with a-type base-stacking
Hormeño S., Ibarra B., Carrascosa J.L., Valpuesta J.M., Moreno-Herrero F., Arias-Gonzalez JR.
Biophysical Journal 100(8): 1996-2005
2011
Condensation prevails over B-A transition in the structure of DNA at low humidity
Hormeño S., Moreno-Herrero F., Ibarra B., Carrascosa J.L., Valpuesta J.M., Arias-Gonzalez J.R.
Biophysical Journal 100(8): 2006-2015
2011
Mechanical properties of high-G.C content DNA with a-type base-stacking
Hormeño S., Ibarra B., Carrascosa J.L., Valpuesta J.M., Moreno-Herrero F., Arias-Gonzalez JR.
Biophysical Journal, 2011, 100(8): 1996-2005
2011
Condensation prevails over B-A transition in the structure of DNA at low humidity
Hormeño S., Moreno-Herrero F., Ibarra B., Carrascosa J.L., Valpuesta J.M., Arias-Gonzalez J.R.
Biophysical Journal, 2011 100(8): 2006-2015
2009
Proofreading Dynamics of a Processive DNA Polymerase
Ibarra, B., Chemla Y., Plyasunov, S., Smith S.B., Salas M., Bustamante C.
EMBO Journal 28: 2794-2802
2009
Single centrosome manipulation reveals its electric charge and associated dynamic structure
Hormeño S., Ibarra B., Chichón F., Habermann K., Lange B., Valpuesta J.M., Carrascosa J.L., Arias-González J.R.
Biophysical Journal 97: 1022-1030
2009
Proofreading Dynamics of a Processive DNA Polymerase
Ibarra, B., Chemla Y., Plyasunov, S., Smith S.B., Salas M., Bustamante C.
EMBO Journal, 2009, 28: 2794-2802
2009
Single centrosome manipulation reveals its electric charge and associated dynamic structure
Hormeño S., Ibarra B., Chichón F., Habermann K., Lange B., Valpuesta J.M., Carrascosa J.L., Arias-González J.R.
