Publications - LUMICKS

Publications

Read the latest publications from LUMICKS instrument users

Be it big or small. Great science is our ultimate goal.

DNA/RNA–protein interactions publications

Lin, SN. et al. Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions . Scientific Reports, 2021
Losito, M. et al. Cas12a Target Search and Cleavage on Force-Stretched DNA. PCCP, 2021
Newton, M. D. et al. A Minimal Load-and-Lock Ru^II Luminescent DNA Probe. Angew. Chem. Int. Ed, 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, 2021
de Asis Balaguer, F. et al. CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion from parS. eLife, 2021
Quail, T. et al. Force generation by protein–DNA co-condensation. Nature Physics, 2021
Belan, O. et al. Generation of versatile ss-dsDNA hybrid substrates for single-molecule analysis. STAR Protocols, 2021
Keenen, M. M. et al. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. eLife, 2021.
Renger, R. et al. Co-condensation of proteins with single- and double-stranded DNA. bioRxiv, 2021.
Belan, O. et al. Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins. Molecular Cell, 2021.
Sánchez, H. et al. DNA replication origins retain mobile licensing proteins. Nature Communications, 2021.
Ye, S. et al. Proximal Single-Stranded RNA Destabilizes Human Telomerase RNA G-Quadruplex and Induces Its Distinct Conformers . J. Phys. Chem. Lett, 2021.
Lin, X. et al. Cooperative DNA looping by PRC2 complexes. Nucleic Acids Research, 2021.
Kretzer, B. et al. Single-Molecule Mechanics in Ligand Concentration Gradient. Micromachines, 2020.
Qin, Z. et al. Human RPA activates BLM’s bidirectional DNA unwinding from a nick. eLife, 2020.
Rill, N. et al. Alkyltransferase-like protein clusters scan DNA rapidly over long distances and recruit NER to alkyl-DNA lesions. PNAS, 2020.
Khawaja, A. et al. Distinct pre-initiation steps in human mitochondrial translation. Nature Communications, 2020.
Spakman, D. et al. Constructing arrays of nucleosome positioning sequences using Gibson Assembly for single-molecule studies. Scientific Reports, 2020.
Zhang, S. et al. Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation. EMBO Rep, 2020.
Newton, M. et al. DNA stretching induces Cas9 off-target activity. Nature Structural & Molecular Biology, 2019.
Zheng, Q. et al. Reversible histone glycation is associated with disease-related changes in chromatin architecture. Nature Communications, 2019.
Kosinski R. et al. Sites of high local frustration in DNA origami. Nature Communications, 2019.
Wasserman, M. et al.Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. Cell, 2019.
Marchetti, M. et al.Real-Time Assembly of Viruslike Nucleocapsids Elucidated at the Single-Particle Level. Nano Letters, 2019.
Gutierreu-Flux^™Escribano, P. et al.A conserved ATP- and Scc2/4-dependent activity for cohesin in tethering DNA molecules. Science Advances, 2019.
Zhang, Q. et al. The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation. Science Advances, 2019.
Leicher, R. et al. Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. PNAS, 2019.

Cellular structure and transport publications

Schepers, A. V. et al. Multiscale mechanics and temporal evolution of vimentin intermediate filament networks. PNAS, 2021
Budaitis, B. G. et al. Pathogenic Mutations in the Kinesin-3 Motor KIF1A Diminish Force Generation and Movement Through Allosteric Mechanisms. bioRxiv, 2021.
Lam, A. J. et al. A Highly Conserved 310-Helix Within the Kinesin Motor Domain is Critical for Kinesin Function and Human Health. bioRxiv, 2021.
Kučera, O. et al. Anillin propels myosin-independent constriction of actin rings. Nature Communications, 2021
Nguyen, A. et al. Multi-oscillation microrheology via Acoustic Force Spectroscopy enables frequency-dependent measurements on endothelial cells at high-throughput . Lab on a Chip, 2021.
Schaedel, L. et al. Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions. Nature Communications, 2021.
Sorkin, R. et al.Synaptotagmin-1 and Doc2b Exhibit Distinct Membrane-Remodeling Mechanisms. Biophysical Journal, 2020.
Schepers, A. et al. Tuning intermediate filament mechanics by indirect and direct charge variations. Nanoscale, 2020.
Mei, L. et al. Molecular mechanism for direct actin force-sensing by α-catenin. eLife, 2020.
Kraxner, J. et al. Post-Translational Modifications Soften Vimentin Intermediate Filaments. Nanoscale, 2020.
Kučera, O. et al. Anillin propels myosin-independent constriction of actin rings. bioRxiv, 2020.
Forsting, J. et al. Vimentin Intermediate Filaments Undergo Irreversible Conformational Changes during Cyclic Loading. Nano Letters, 2019.
Lorenz, C. et al. Lateral Subunit Coupling Determines Intermediate Filament Mechanics. Physical Review Letters, 2019.
Block, J. et al. Viscoelastic properties of vimentin originate from nonequilibrium conformational changes. Science Advances, 2018.
Block, J. et al. Nonlinear Loading-Rate-Dependent Force Response of Individual Vimentin Intermediate Filaments to Applied Strain. Physical Review Letters, 2017.

Protein droplets and phase separation publications

Ghosh, A. et al. Shear relaxation governs fusion dynamics of biomolecular condensates. Nature Communications, 2021.
Alshareedah, I. et al. Quantifying Viscosity and Surface Tension of Multi-Component Protein-Nucleic Acid Condensates. Biophysical Journal, 2021.
Rhine, K. et al. Single-molecule and ensemble methods to probe RNP nucleation and condensate properties. Methods, 2021.
Alshareedah, I. et al. Phase transition of RNA−protein complexes into ordered hollow condensates. PNAS, 2020.
Ghosh, A. and Zhou, H.-X. Determinants for Fusion Speed of Biomolecular Droplets. The Journal of Physical Chemistry B, 2020.
Jawerth, L. et al. Protein condensates as aging Maxwell fluids. Science, 2020.
Kaur, T. et al. Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies. bioRxiv, 2020.
Kaur, T. et al. Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates. Biomolecules, 2019.
Gui, X., et al. Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly. Nature Communications, 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, 2019.
Jawerth, L. et al. Salt-Dependent Rheology and Surface Tension of Protein Condensates Using Optical Traps. Physical Review Letters, 2018.

Protein folding and conformational changes publications

Maciuba, K. et al. Facile tethering of stable and unstable proteins for optical tweezers experiments. Biophysical Journal, 2021.
Wruck, F. et al. The ribosome modulates folding inside the ribosomal exit tunnel. bioRxiv, 2021.
Avellaneda, M. et al. Simultaneous sensing and imaging of individual biomolecular complexes enabled by modular DNA–protein coupling. Communications Chemistry, 2020.
Avellaneda, M. et al. Processive extrusion of polypeptide loops by a Hsp100 disaggregase. Nature, 2020.

Immuno-oncology publications

Fernandez de Larrea C. et al. Defining an Optimal Dual-Targeted CAR T-cell Therapy Approach Simultaneously Targeting BCMA and GPRC5D to Prevent BCMA Escape-Driven Relapse in Multiple Myeloma. Blood Cancer Discovery, 2020.
Kamsma D. et al. Single-Cell Acoustic Force Spectroscopy: Resolving Kinetics and Strength of T Cell Adhesion to Fibronectin. Cell Reports, 2018.

Other DSM application publications

Vasse, G. F. et al. Single Cell Reactomics: Real‐Time Single‐Cell Activation Kinetics of Optically Trapped Macrophages. small methods, 2021.
Dai, X. et al. Optical tweezers-controlled hotspot for sensitive and reproducible surface-enhanced Raman spectroscopy characterization of native protein structures. Nature Communications, 2021.