+34 912998863 borja.ibarra@gmail.com



The use of nanomotors to power molecular machines is one of the most exciting challenges facing nanotechnology. Our laboratory uses nanoscale principles and techniques to understand at the molecular level the physical-chemical and mechanistic principles of operation of biological and synthetic molecular motors. Using nature as a guide will facilitate the design of highly efficient ‘man-made’ molecular machines for complex operations at the nanoscale.


Interested in ubiquitous SSB?? Check this out!

New volume of Methods and Molecular Biology on Single Stranded DNA Binding Proteins edited by Marcos Oliveira. This volume provides a comprehensive set of protocols that can be used by any research lab to investigate diverse functional and structural properties of...

Recent Publications

Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB

Plaza-G.A. IsmaelKateryna M. LemishkoRodrigo CrespoThinh Q. TruongLaurie S. KaguniFrancisco J. Cao-GarcíaGrzegorz L. CiesielskiBorja Ibarra

Nucleic Acid Res.  2023 Feb 28;51(4):1750-1765. doi: 10.1093/nar/gkad037.

In vitro single-molecule manipulation studies of viral DNA replication.

Bocanegra R, Plaza G-A I,Ibarra B.

Enzymes. 2021;49:115-148. DOI: 10.1016/bs.enz.2021.09.001

Cooperativity-Dependent Folding of Single-Stranded DNA

Viader-Godoy, X. and Pulido, C. R. and Ibarra, B. and Manosas, M. and Ritort, F.

Phys. Rev. X 11, 031037  (2021)

DNA replication machinery: Insights from in vitro single-molecule approaches.

Rebeca Bocanegra, Ismael Plaza G.A., Carlos R.Pulido, Borja Ibarra (2021)

Computational and Structural Biotechnology Journal Volume 19, 2021, Pages 2057-2069

Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-Binding Protein-DNA Complexes.

Morin J.A., Cerrón F., Cao-García F.J., Ibarra B. (2021)

Single Stranded DNA Binding Proteins. Methods in Molecular Biology, vol 2281, 2021 

Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins.

Cerrón F., Ibarra B. (2021)

Single Stranded DNA Binding Proteins. Methods in Molecular Biology, vol 2281.  2021

Five minutes in the life of a molecular shuttle:near-equilibrium measurements of shuttling dynamics with optical tweezers

Kateryna M Lemishko, Teresa Naranjo, Emilio. M Pérez, Borja Ibarra (2020)

Building and Probing Small for Mechanics. Springer Nature.2020

Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes

Alberto Marin-GonzalezCesar L. PastranaRebeca BocanegraAlejandro Martín, GonzálezJ.G. VilhenaRubén PérezBorja IbarraClara Aicart-RamosFernando Moreno-Herrero

Nucleic Acids Research, April 13, 2020

Dynamic constriction and fission of ER membranes by reticulon

Javier Espadas, Diana Pendin, Rebeca Bocanegra, et al

Nature Communications, Volume 10, Article number: 5327 (2019)

Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis

Cerron, Fernando; de Lorenzo, Sara; Lemishko, Kateryna; Ciesielski, Grzegorz ; Kaguni, Laurie; Cao, Francisco; Ibarra, Borja.

Nucleic Acids Research,  47(11), 5723–5734 (2019)

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)

DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein.

JA Morin, F Cerrón, J Jarillo, E Beltrán-Heredia, GL Ciesielski, JR Arias-Gonzalez, LS Kaguni, FJ Cao, B Ibarra.

Nucleic Acids Research, 45(12), 7237-7248, (2017)

Mechanical measurement of hydrogen-bonded host-guest systems under non-equilibrium, near-physiological conditions.

T. Naranjo, F. Cerrón, B. Nieto-Ortega, A Latorre, A Somoza, B. Ibarra*, M. Pérez*
*corresponding authors

Chemical Science, 8, 6037-6041, (2017).
Highlighted by the Royal Society of Chemistry in Chemistry World

Mechanics, Thermodynamics, and kinetics of ligand binding to biopolymers.

J. Jarillo, E. Beltrán, J Morín, J.P. García-Villaluenga, B. Ibarra, F. Cao

PLoS ONE 12(4): e0174830 (2017)

Kinetic modeling of molecular motors: pause model and parameter determination from single molecule experiments.

Morin J.A. ,Ibarra B. ,Cao F.J.

Journal of Statistical Mechanics: Theory and Experiments 2016(5) 054031

Mechano-chemical kinetics of DNA replication: identification of the translocation step of a replicative DNA polymerase.

J.A. Morín, F.J. Cao, J.M. Lázaro, J.R. Arias-Gonzalez, J.M. Valpuesta, J.L. Carrascosa, M. Salas and B. Ibarra.

Nucleic Acids Research 43(7), 3643-3652 (2015)

Manipulation of single polymerase-DNA complexes: a mechanical view of DNA unwinding during replication.

J.A. Morin, F.J. Cao, J.M. Valpuesta, J.L. Carrascosa, M. Salas, B. Ibarra.

Cell Cycle 11(16), 2967-2968 (2012)

Active DNA unwinding dynamics during processive DNA replication.

J.A. Morín, 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), 8115-8120, (2012)

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 J.R.

Biophysical Journal 100(8), 1996-2005, (2011)

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)