Publications
Explore a range of publications within our dynamic single-molecule application field
- DNA–binding proteins
- Protein folding
- Cytoskeletal structure and transport
- Phase separation
- Mechanobiology
- Other applications
- Newton, M. et al. DNA stretching induces Cas9 off-target activity. Nature Structural & Molecular Biology (David Rueda, Imperial College London) 2019
- Zheng, Q. et al. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nature Communications (Shixin Liu, Rockefeller University and Yael David MSKCC) 2019
- Kosinski R. et al. Sites of high local frustration in DNA origami. Nature Communications (Barbara Saccà, University of Essen-Duisburg) 2019
- Wasserman, M. et al.Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. Cell (Shixin Liu & Michael O’Donnel, Rockefeller University) 2019
- Marchetti, M. et al.Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level. Nano Letters (Gijs Wuite, VU University Amsterdam & Wouter Roos, Rijksuniversiteit Groningen) 2019
- Leicher, R. et al. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. PNAS (Shixin Liu, Rockefeller University) 2019
- Kretzer, B. et al. Single-Molecule Mechanics in Ligand Concentration Gradient. Micromachines (Miklós Kellermayer, Semmelweis University) 2020
- Qin, Z. et al. Human RPA activates BLM’s bidirectional DNA unwinding from a nick. eLife (Bo Sun, ShanghaiTech) 2020
- Rill, N. et al. Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions. PNAS (Ingrid Tessmer, University of Würzburg) 2020
- Khawaja, A. et al. Distinct pre-initiation steps in human mitochondrial translation. Nature Communications (Joanna Rorbach, Karolinska Institute) 2020
- Spakman, D. et al. Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies. Scientific Reports (Gijs Wuite, VU University Amsterdam) 2020
- Zhang, S. et al. Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation. EMBO Rep (Bo Sun, ShanghaiTech) 2020
- Belan, O. et al. Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins. Molecular Cell (David Rueda, Imperial College London) 2021
- Keenen, M. M. et al. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife (Sy Redding, University of California San Francisco) 2021
- Ye, S. et al. Proximal Single-Stranded RNA Destabilizes Human Telomerase RNA G-Quadruplex and Induces Its Distinct Conformers. J. Phys. Chem. Lett. (Bo Sun, ShanghaiTech) 2021
- Lin, X. et al. Cooperative DNA looping by PRC2 complexes. Nucleic Acids Research (Shixin Liu, Rockefeller University) 2021
- Belan, O. et al. Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis. STAR Protocols (David Rueda, Imperial College London) 2021
- Quail, T. et al. Force generation by protein–DNA co-condensation. Nature Physics (Stephan Grill, TU Dresden) 2021
- de Asis Balaguer, F. et al. CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS. eLife (Fernando Moreno-Herrero, Centro Nacional de Biotecnología) 2021
- Backer, A. S. et al. Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy. J. Phys. Chem. B (Gijs Wuite, VU University Amsterdam) 2021
- Buzón, P. et al. Virus self-assembly proceeds through contact-rich energy minima. Science Advances (Gijs Wuite, VU University Amsterdam & Wouter Roos, Rijksuniversiteit Groningen) 2021
- Zhang, Q. et al. Efficient DNA interrogation of SpCas9 governed by its electrostatic interaction with DNA beyond the PAM and protospacer. Nucleic Acids Research (Bo Sun, ShanghaiTech) 2021
- Hill, C. H. et al. Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Nature Communications (Neva Caliskan, Helmholtz Institute for RNA-based infection research (HIRI), University of Würzburg & Ian Brierly, University of Cambridge) 2021
- Paul, B. et al. Mechanics of CRISPR-Cas12a and engineered variants on λ-DNA. Nucleic Acids Research (Guillermo Montoya, University of Copenhagen) 2021
- Anand, R. et al. HELQ is a dual-function DSB repair enzyme modulated by RPA and RAD51. Nature (Simon Boulton, Crick Institute) 2021
- Losito, M. et al. Cas12a Target Search and Cleavage on Force-Stretched DNA. PCCP (David Rueda, Imperial College London) 2021
- Sánchez, H. et al. DNA replication origins retain mobile licensing proteins. Nature Communications (Nynke Dekker, TU Delft) 2021
- Renger, R. et al.,Co-condensation of proteins with single- and double-stranded DNA. PNAS (Stephan Grill, TU Dresden) 2022
- Morin, J. A. et al. Sequence-dependent surface condensation of a pioneer transcription factor on DNA. Nature Physics (Stephan Grill, TU Dresden) 2022
- Bernacchia L. et al, Identification of the target and mode of action for the prokaryotic nucleotide excision repair inhibitor ATBC, Biosci Rep (Niel Kad, Kent University) 2022
- Bi L. et al, The convergence of head-on DNA unwinding forks induces helicase oligomerization and activity transition, PNAS (Bo Sun, ShanghaiTech) 2022
- Gien, H. et al. HIV-1 Nucleocapsid Protein Binds Double-Stranded DNA in Multiple Modes to Regulate Compaction and Capsid Uncoating. Viruses (Mark Williams, Northeastern University) 2022
- Lijuan, Guo. et al. Stochastically multimerized ParB orchestrates DNA assembly as unveiled by single-molecule analysis. Nucleic Acid Research. (Bo Sun, ShanghaiTech) 2022
- Li, S. et al. Nucleosome-directed replication origin licensing independent of a consensus DNA sequence. Nature Communications. (Shixin Liu, Rockefeller University) 2022
- Kuppa, et al. Rtt105 regulates RPA function by configurationally stapling the flexible domains. Nature Communications. (Edwin Antony and Taekjip Ha, Johns Hopkins University) 202
- Carcamo, C. C. et al. ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA. eLife (Taekjip Ha, Johns Hopkins University) 2022
- Kaczmarczyk A. et al. Search and processing of Holliday junctions within long DNA by junction-resolving enzymes. Nature Communication (David Rueda, Imperial College) 2022
- Li et al., Origin recognition complex harbors an intrinsic nucleosome remodeling activity. PNAS (Shixin Liu, Rockefeller University) 2022
- J.Chang et al., Smc5/6’s multifaceted DNA binding capacities stabilize branched DNA structures. Nature Communication (Shixin Liu, Rockefeller University) 2022
- Spakman et al., PICH acts as a force dependent nucleosome remodeler. Nature communications (Gijs Wuite, VU) 2022
- Belan O. et al., POLQ seals post-replicative ssDNA gaps to maintain genome stability in BRCA-deficient cancer cells. Molecular Cell (Simon Boulton, Crick Institute) 2022
- Jang S. et al., Cooperative interaction between AAG and UV-DDB in the removal of modified bases. NAR (Ben Van Houten, University of Pittsburgh) 2022
- McCauley, M. et al., Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes. Cell Reports (Mark Williams, Northeastern University) 2022
- N. Tanasie et al., Stabilization of DNA fork junctions by Smc5/6 complexes revealed by single-molecule imaging. Cell Reports (Johannes Stigler, LMU & Luis Aragon, Imperial College London) 2022
- Schaich M. et al., Single-molecule analysis of DNA-binding proteins from nuclear extracts (SMADNE). NAR (Ben Van Houten, University of Pittsburgh) 2023
- Ling Wang et. al., Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. Molecular Cell (Shixin Liu, Rockefeller University) 2023
- Kacey N.Mersch “Helicase” activity promoted through dynamic interactions between a ssDNA translocase and a diffusing SSB protein. PNAS (Timothy M. Loham, St. Louis) 2023
- Daniel Ramírez Montero, Nucleotide binding halts diffusion of the eukaryotic replicative helicase during activation Nature Communications, (Nynke Dekker, TU Delft) 2023
- Greenhough L. A. et al, Structure and mechanism of action of the RAD51BCD-XRCC2 tumour suppressor complex, Nature, (Simon Boulton & Steve West, Crick) 2023
- Avellaneda, M. et al.Processive extrusion of polypeptide loops by a Hsp100 disaggregase. Nature (Sander Tans, AMOLF) 2020
- Avellaneda, M. et al.Simultaneous sensing and imaging of individual biomolecular complexes enabled by modular DNA–protein coupling. Communications Chemistry (Sander Tans, AMOLF) 2020
- Wruck, F. et al. The ribosome modulates folding inside the ribosomal exit tunnel. Communications Biology (Sander Tans, AMOLF) 2021
- Maciuba, K. et al. Facile tethering of stable and unstable proteins for optical tweezers experiments. Biophysical Journal (Christian Kaiser, Johns Hopkins University) 2021
- Zimmer, M. M. et al. The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting. Nature Communications (Neva Caliskan, Helmholtz Institute for RNA-based infection research (HIRI), University of Würzburg) 2021
- Pekarek L et al., Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation, JoVE (Neva Caliskan, HIRI) 2022
- Naqvi, M. et al. Protein chain collapse modulation and folding stimulation by GroEL-ES, Sci. Advances (Sander Tans, AMOLF) 2022
- Liu, J. et al. Minimalist design of polymer-oligopeptide hybrid as intrinsically disordered protein-mimicking scaffold for artificial membraneless organelle. ACS Cent. Sci. (Jinqing Huang, Hong Kong University) 2022
- Buck, S. et al. POTATO: An automated pipeline for batch analysis of optical tweezers data. Biophysical Journal (Neva Caliskan, Helmholtz Institute for RNA-based infection research (HIRI), University of Würzburg) 2022
- Walker, S. D. et al, The activated ClpP peptidase forcefully grips a protein substrate. Biophysical Journal (Adrian Olivares, Vanderbilt University) 2022
- Freitag M. et al., Single-molecule experiments reveal the elbow as an essential folding guide in SMC coiled-coil arms. Biophysical Journal (Johannes Stigler, LMU) 2022
- Pekarek L. et al., Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function. NAR (Neva Caliskan, HIRI) 2022
- Block, J. et al. Nonlinear Loading-Rate-Dependent Force Response of Individual Vimentin Intermediate Filaments to Applied Strain. Physical Review Letters (Sarah Köster, University of Göttingen) 2017
- Block, J.et al. Viscoelastic properties of vimentin originate from nonequilibrium conformational changes. Science Advances (Sarah Köster, University of Göttingen) 2018
- Forsting, J. et al.Vimentin Intermediate Filaments Undergo Irreversible Conformational Changes during Cyclic Loading. Nano Letters (Sarah Köster, University of Göttingen) 2019
- Lorenz, C. et al.Lateral Subunit Coupling Determines Intermediate Filament Mechanics. Physical Review Letters (Sarah Köster, University of Göttingen) 2019
- Gutierrez-Escribano, et al. A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules. Science Advances (David Rueda, & Luis Aragon, Imperial College London) 2019
- Zhang, Q. et al. The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation.Science Advances (Bo Sun, ShanghaiTech) 2019
- Sorkin, R. et al.Synaptotagmin-1 and Doc2b Exhibit Distinct Membrane-Remodeling Mechanisms. Biophysical Journal (Gijs Wuite, VU University Amsterdam & Wouter Roos, Rijksuniversiteit Groningen) 2020
- Schepers, A. et al. Tuning intermediate filament mechanics by indirect and direct charge variations. Nanoscale (Sarah Köster, University of Göttingen) 2020
- Mei, L. et al. Molecular mechanism for direct actin force-sensing by α-catenin. eLife (Shixin Liu & Gregory M. Alushin, Rockefeller University) 2020
- Kraxner, J. et al. Post-Translational Modifications Soften Vimentin Intermediate Filaments. Nanoscale (Sarah Köster, University of Göttingen) 2020
- Budaitis, B. G. et al. Pathogenic Mutations in the Kinesin-3 Motor KIF1A Diminish Force Generation and Movement Through Allosteric Mechanisms. Journal of Cell Biology (Arne Gennerich, Albert Einstein College of Medicine) 2021
- Lam, A. J. et al. A Highly Conserved 310-Helix Within the Kinesin Motor Domain is Critical for Kinesin Function and Human Health. Science Advances (Arne Gennerich, Albert Einstein College of Medicine) 2021
- Schaedel, L. et al. Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions. Nature Communications, (Sarah Köster, University of Göttingen) 2021
- Kučera, O. et al. Anillin propels myosin-independent constriction of actin rings. Nature Communications (Zdenek Lansky, BIOCEV) 2021
- Schepers, A. V. et al. Multiscale mechanics and temporal evolution of vimentin intermediate filament networks. PNAS, (Sarah Köster, University of Göttingen) 2021
- Jawerth, L. et al. Salt-Dependent Rheology and Surface Tension of Protein Condensates Using Optical Traps. Physical Review Letters (Tony Hyman, MPI-CBG) 2018
- Kaur, T. et al. Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates. Biomolecules (Priya Banerjee, University at Buffalo) 2019
- Gui, X., et al. Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly. Nature Communications (Bo Sun, ShanghaiTech & Cong Liu, CAS-SIOC) 2019
- Alshareedah, I. et al. Interplay between Short-Range Attraction and Long-Range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein–RNA Complexes. Journal of the American Chemical Society (Priya Banerjee, University at Buffalo) 2019
- Alshareedah, I. et al. Phase transition of RNA−protein complexes into ordered hollow condensates. PNAS (Priya Banerjee, University at Buffalo) 2020
- Ghosh, A. and Zhou, H.-X. Determinants for Fusion Speed of Biomolecular Droplets. The Journal of Physical Chemistry B (Huan-Xiang Zhou, University of Illinois Chicago) 2020
- Jawerth, L. et al. Protein condensates as aging Maxwell fluids. Science (Tony Hyman, MPI-CBG) 2020
- Alshareedah, I. et al. Quantifying Viscosity and Surface Tension of Multi-Component Protein-Nucleic Acid Condensates. Biophysical Journal (Priya Banerjee, University at Buffalo) 2021
- Kaur, T. et al. Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Morphologies. Nature Communications (Priya Banerjee, University at Buffalo) 2021
- Rhine, K. et al. Single-molecule and ensemble methods to probe RNP nucleation and condensate properties. Methods (Sua Myong, Johns Hopkins University) 2021
- Newton, M. D. et al. A Minimal Load-and-Lock Ru Luminescent DNA Probe. Angew. Chem. Int. Ed. (David Rueda, Imperial College London) 2021
- Lin, SN. et al. Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions. Scientific Reports (Gijs Wuite, VU University Amsterdam) 2021
- Alshareedah, I. et al. Programmable viscoelasticity in protein-RNA condensates with disordered sticker-spacer polypeptides. Nature Communications (Priya Banerjee, University at Buffalo) 2021
- Ghosh, A. et al. Shear relaxation governs fusion dynamics of biomolecular condensates. Nature Communications, (Huan-Xiang Zhou, University of Illinois Chicago) 2021
- Joris Van Lindt et al., F/YGG-motif is an intrinsically disordered nucleic-acid binding motif. RNA biology (Leuven) 2022
- Manjia Li. et al, Controlling synthetic membraneless organelles by a red-light-dependent singlet oxygen-generating protein. Nature Communication (Jingqing Huang, HKUST) 2022
- Kota, D, et al. Macromolecular Regulation of the Material Properties of Biomolecular Condensates. The Journal of Physical Chemistry Letters (Huan-Xiang Zhou, University of Illinois Chicago) 2022
- Teng, Wang.et al. Bloom syndrome helicase compresses single-stranded DNA into phase-separated condensates. Angewandte Chemie International Edition (Bo Sun, ShanghaiTech) 2022
- Vasse, G. F. et al. Single Cell Reactomics: Real‐Time Single‐Cell Activation Kinetics of Optically Trapped Macrophages. small methods, (Wouter Roos, Rijksuniversiteit Groningen) 2021
- Evers, T. M. J. et al. Single-cell analysis reveals chemokine-mediated differential regulation of monocyte mechanics. iScience, (Alireza Mashaghi , Leiden University) 2022
- Sheikhhassani, V. et al., Single cell force spectroscopy of erythrocytes at physiological and febrile temperatures reveals mechano-modulatory effects of atorvastatin. Soft matter, (Mashaghi, Leiden) 2022
- Kono S. et al., Resolving the subtle details of human DNA alkyltransferase lesion search and repair mechanism by single-molecule studies. PNAS, (Tessmer, Würzburg) 2022
- Chardon F. et al., CENP-B-mediated DNA loops regulate activity and stability of human centromeres, Molecular Cell (Fachinetti, Institute Curie) 2022
- Hormeno S. et al, Human HELB is a processive motor protein that catalyzes RPA clearance from single-stranded DNA, Elife, (Moreno, CNB, Madrid) 2022
- Evers T. et al., Single-Cell Mechanical Characterization of Human Macrophages. Advanced Nanobiomed Research (Alireza, Leiden University) 2022
- Mulla, Y. et al. Weak catch bonds make strong networks. Nature Materials (Sander Tans, AMOLF & Gijsje Koenderink, TU Delft) 2022
- Siahaan, V. et al. Microtubule Lattice Spacing Governs Cohesive Envelope Formation of Tau Family Proteins. Nature Chemical Biology (Zdenek Lansky, BIOCEV) 2022
- Dharan R. et al., Transmembrane proteins tetraspanin 4 and CD9 sense membrane curvature. PNAS (Raya Sorkin, Tel Aviv) 2022
- Quikun Y. et al., Directed assembly of genetically engineered eukaryotic cells into living functional materials via ultrahigh-affinity protein interactions. Sci. Advances (Jinqing Huang, Hong Kong UST) 2022
- Goren S. et al., Probing Local Force Propagation in Tensed Fibrous Gels, Small (Raya Sorkin, Tel Aviv) 2022
- Stadler R. et al., A circular zone of attachment to the extracellular matrix provides directionality to the motility of Toxoplasma gondii in 3D. Elife (Gary E. Ward, Vermont University) 2022
- Zhorabek F. et al., Construction of multiphasic membraneless organelles towards spontaneous spatial segregation and directional flow of biochemical reactions. Chemical Science (Jinqing Huang, Hong Kong UST) 2023
- Cheng Lyu et al., Advanced glycation end-products as mediators of the aberrant crosslinking of extracellular matrix in scarred liver tissue. Nature Biomedical Engineering (Yanan Du, Tsinghua university) 2023
- Dai, X. et al. Optical tweezers-controlled hotspot for sensitive and reproducible surface-enhanced Raman spectroscopy characterization of native protein structures. Nature Communications (Jinqing Huang, Hong Kong University of Science and Technology) 2021
- Freitag, M. et al. Identification and correction of miscalibration artifacts based on force noise for optical tweezers experiments. J. Chemical Physics (Johannes Stigler, LMU) 2021
- Molcrette B, et al. Experimental study of a nanoscale translocation ratchet. PNAS (Fabien Montel, École Normale Supérieure Lyon) 2022
- Cheppali S., Supported Natural Membranes on Microspheres for Protein–Protein Interaction Studies. ACS Appl. Mater. Interfaces, (Raya Sorkin, Tel Aviv) 2022
- Dharan R., Tetraspanin 4 stabilizes membrane swellings and facilitates their maturation into migrasomes. Nature communications (Raya Sorkin, Tel Aviv) 2023
Our solution
The C-Trap® Optical Tweezers – Fluorescence & Label-free Microscopy is the world’s first instrument that allows simultaneous manipulation and visualization of single-molecule interactions in real time. It combines high resolution optical tweezers, fluorescence and label-free microscopy and an advanced microfluidics system in a truly integrated and correlated solution.
The C-Trap offers you a fast workflow to seamlessly catch and manipulate single molecules. The instrument measures their structural changes or interactions while you visualize them in teal time with high spatial and temporal resolution, ultimately offering you a complete and detailed picture of biomolecular properties and interactions
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