MOLECULAR MOTORS
MANIPULATION LAB
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.
Research
News
We are very grateful to the CAIXA RESEARCH HEALTH program for funding MITO4NEURO. This project represents a truly multidisciplinary approach to study the human mitochondrial DNA replisome in health and disease.
We are very grateful to the CAIXA RESEARCH HEALTH program for funding MITO4NEURO. This project represents a truly multidisciplinary approach to study the human mitochondrial DNA replisome in health and disease.
We’re excited to share our latest research uncovering the real-time kinetics and regulation of Twinkle, the human mitochondrial DNA helicase -https://doi.org/10.1038/s41467-025-60289-0
WE ARE HIRING!!! Looking for Postdoctoral Research Assisitant to study the operational dynamics of the human mitochondrial replisome. Click for details.
IMDEA Nanociencia, Madrid, Spain. Duration: 2-3 years We are looking to hire a Postdoctoral Research Assistant for an exciting project aimed to understand the dynamics of the human DNA replication in health and disease at the single-molecule level. Our lab...
Interested in Influenza A replication? We have used HSAFM to follow the conformational dynamics of Influenza RNPs during RNA sysnthesis. Check it out
DOI: 10.1021/acsnano.4c01362 Viral ribonucleoproteins (vRNPs) are the cornerstones of viral proliferation, as they form the macromolecular complexes that are responsible for the transcription and replication of most...
Check our new work about how the mitochondrial polymerase and SSB coordinate their activities
https://doi.org/10.1093/nar/gkad037 Many replicative DNA polymerases couple DNA replication and unwinding activities to perform strand displacement DNA synthesis, a critical ability for DNA metabolism. Strand displacement is tightly regulated by partner proteins, such...
It’s not OK for us to say it, but we’ve written a great review about in singulo studies on DNA replication. Check it out!
Click here to enjoy!!
Recent Publications
Auto-regulation of the real-time kinetics of the human mitochondrial replicative helicase
I. Plaza-G.A., M. Ortiz-Rodríguez, S. Buchanan, S Míguez, K Lemishko, F. Moreno-Herrero, R. Fernandez-Leiro, G.L. Ciesielski, B. Ibarra
Nat Commun 16, 5460 (2025).
Transition-path times of molecular shuttles under mechanical equilibrium show symmetry
Tomás Nicolás-García, Natalia Martín Sabanés , Rebeca Bocanegra, R. Dean Astumian, Emilio Perez, and Borja Ibarra
Chem, Volume 11, Issue 6, 102410. 2024
Conformational Dynamics of Influenza A Virus Ribonucleoprotein Complexes during RNA Synthesis
Diego Carlero, Shingo Fukuda, Rebeca Bocanegra, Toshio Ando, Jaime Martin-Benito, and Borja Ibarra
ACS Nano 2024, 10.1021/acsnano.4c01362
Mechanism of strand displacement DNA synthesis by the coordinated activities of human mitochondrial DNA polymerase and SSB
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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.
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
Building and Probing Small for Mechanics. Springer Nature.2020
Understanding the paradoxical mechanical response of in-phase A-tracts at different force regimes
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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.
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
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.
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.
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.
Proofreading Dynamics of a Processive DNA Polymerase.
Ibarra B. ,Chemla Y. ,Plyasunov S. ,Smith S.B. ,Salas M. ,Bustamante, C.
