MOLECULAR MOTORS
MANIPULATION LAB
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.
Research
News
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!!
Have a look to our first ever single-molecule fluorescence results with Lumicks C-trap
We are using the new and fancy Lumicks Ctrap at Fernando Moreno' lab (CNB) to track the real-time kinetics of Pfh1 helicase moving along single stranded DNA. The image above shows the trajectory of a single helicase (blue) tagged with a quantum dot along...
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...
Do you wanna know how our mitochondrial DNApol deals with SSBs?
Check out our recent work at NAR!!
Our lab funded by the Spanish Ministry of Science for 3 more years , 2019-2021!!
Our work on molecular shuttles selected as Nature Communication editor’s highligth!
Recent Publications
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.
