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Xu W, Collette D, Qian J, Finzi L, Dunlap D. Insights on the effect of macromolecular crowding on transcription and its regulation. QRB DISCOVERY 2025; 6:e16. [PMID: 40395559 PMCID: PMC12088913 DOI: 10.1017/qrd.2025.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2024] [Revised: 03/10/2025] [Accepted: 03/15/2025] [Indexed: 05/22/2025] Open
Abstract
Transcription of DNA into RNA is a fundamental cellular process upon which life depends. It is tightly regulated in several different ways, and among the most important mechanisms are protein-induced topological changes in DNA such as looping. In vivo neither transcription, nor protein-induced looping dynamics exhibited by individual molecules are easily monitored. In vitro single-molecule approaches do offer that possibility, but assays are conducted in rarefied, saline buffer conditions which greatly differ from the crowded intracellular environment. In the following, we describe monitoring both transcription and lac repressor-mediated DNA looping of single DNA molecules in the presence of different concentrations of crowders to bridge the gap between in vitro and in vivo experimentation. We found that crowding shifts the preferred orientation of DNA strands in the looped complex. Crowding also attenuates the rate of transcript elongation and enhances readthrough at the terminator. Clearly, the activities of proteins involved in gene regulation are modified in surprising ways by crowding.
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Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
- Institute of STEM Cells and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Dylan Collette
- Physics Department, Emory University, Atlanta, GA, USA
- Physics Department, Oglethorpe University, Atlanta, GA, USA
| | - Jin Qian
- Physics Department, Emory University, Atlanta, GA, USA
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
- Department of Physics & Astronomy, Clemson University, SC, USA
| | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
- Department of Physics & Astronomy, Clemson University, SC, USA
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2
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Huhnstock R, Reginka M, Sonntag C, Merkel M, Dingel K, Sick B, Vogel M, Ehresmann A. Three-dimensional close-to-substrate trajectories of magnetic microparticles in dynamically changing magnetic field landscapes. Sci Rep 2022; 12:20890. [PMID: 36463293 PMCID: PMC9719552 DOI: 10.1038/s41598-022-25391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
The transport of magnetic particles (MPs) by dynamic magnetic field landscapes (MFLs) using magnetically patterned substrates is promising for the development of Lab-on-a-chip (LOC) systems. The inherent close-to-substrate MP motion is sensitive to changing particle-substrate interactions. Thus, the detection of a modified particle-substrate separation distance caused by surface binding of an analyte is expected to be a promising probe in analytics and diagnostics. Here, we present an essential prerequisite for such an application, namely the label-free quantitative experimental determination of the three-dimensional trajectories of superparamagnetic particles (SPPs) transported by a dynamically changing MFL. The evaluation of defocused SPP images from optical bright-field microscopy revealed a "hopping"-like motion of the magnetic particles, previously predicted by theory, additionally allowing a quantification of maximum jump heights. As our findings pave the way towards precise determination of particle-substrate separations, they bear deep implications for future LOC detection schemes using only optical microscopy.
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Affiliation(s)
- Rico Huhnstock
- grid.5155.40000 0001 1089 1036Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany ,grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Meike Reginka
- grid.5155.40000 0001 1089 1036Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Claudius Sonntag
- grid.5155.40000 0001 1089 1036Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, 34121 Kassel, Germany
| | - Maximilian Merkel
- grid.5155.40000 0001 1089 1036Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany ,grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Kristina Dingel
- grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany ,grid.5155.40000 0001 1089 1036Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, 34121 Kassel, Germany
| | - Bernhard Sick
- grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany ,grid.5155.40000 0001 1089 1036Intelligent Embedded Systems, University of Kassel, Wilhelmshöher Allee 71-73, 34121 Kassel, Germany
| | - Michael Vogel
- grid.5155.40000 0001 1089 1036Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany ,grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany ,grid.9764.c0000 0001 2153 9986Present Address: Institute for Materials Science, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany
| | - Arno Ehresmann
- grid.5155.40000 0001 1089 1036Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany ,grid.5155.40000 0001 1089 1036Artificial Intelligence Methods for Experiment Design (AIM-ED), Joint Lab of Helmholtzzentrum für Materialien und Energie, Berlin (HZB) and University of Kassel, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
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Bailey MR, Grillo F, Isa L. Tracking Janus microswimmers in 3D with machine learning. SOFT MATTER 2022; 18:7291-7300. [PMID: 36106459 DOI: 10.1039/d2sm00930g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Advancements in artificial active matter systems heavily rely on our ability to characterise their motion. Yet, the most widely used tool to analyse the latter is standard wide-field microscopy, which is largely limited to the study of two-dimensional motion. In contrast, real-world applications often require the navigation of complex three-dimensional environments. Here, we present a Machine Learning (ML) approach to track Janus microswimmers in three dimensions, using Z-stacks as labelled training data. We demonstrate several examples of ML algorithms using freely available and well-documented software, and find that an ensemble Decision Tree-based model (Extremely Randomised Decision Trees) performs the best at tracking the particles over a volume spanning more than 40 μm. With this model, we are able to localise Janus particles with a significant optical asymmetry from standard wide-field microscopy images, bypassing the need for specialised equipment and expertise such as that required for digital holographic microscopy. We expect that ML algorithms will become increasingly prevalent by necessity in the study of active matter systems, and encourage experimentalists to take advantage of this powerful tool to address the various challenges within the field.
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Affiliation(s)
- Maximilian Robert Bailey
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
| | - Fabio Grillo
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093 Zürich, Switzerland.
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Xu W, Yan Y, Artsimovitch I, Dunlap D, Finzi L. Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops. Nucleic Acids Res 2022; 50:2826-2835. [PMID: 35188572 PMCID: PMC8934669 DOI: 10.1093/nar/gkac093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/22/2021] [Accepted: 02/20/2022] [Indexed: 11/30/2022] Open
Abstract
Some proteins, like the lac repressor (LacI), mediate long-range loops that alter DNA topology and create torsional barriers. During transcription, RNA polymerase generates supercoiling that may facilitate passage through such barriers. We monitored E. coli RNA polymerase progress along templates in conditions that prevented, or favored, 400 bp LacI-mediated DNA looping. Tethered particle motion measurements revealed that RNA polymerase paused longer at unlooped LacI obstacles or those barring entry to a loop than those barring exit from the loop. Enhanced dissociation of a LacI roadblock by the positive supercoiling generated ahead of a transcribing RNA polymerase within a torsion-constrained DNA loop may be responsible for this reduction in pause time. In support of this idea, RNA polymerase transcribed 6-fold more slowly through looped DNA and paused at LacI obstacles for 66% less time on positively supercoiled compared to relaxed templates, especially under increased tension (torque). Positive supercoiling propagating ahead of polymerase facilitated elongation along topologically complex, protein-coated templates.
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Affiliation(s)
- Wenxuan Xu
- Physics Department, Emory University, Atlanta, GA, USA
| | - Yan Yan
- Physics Department, Emory University, Atlanta, GA, USA
| | | | - David Dunlap
- Physics Department, Emory University, Atlanta, GA, USA
| | - Laura Finzi
- Physics Department, Emory University, Atlanta, GA, USA
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Carlucci LA, Thomas WE. Modification to axial tracking for mobile magnetic microspheres. BIOPHYSICAL REPORTS 2021; 1:100031. [PMID: 35965968 PMCID: PMC9371438 DOI: 10.1016/j.bpr.2021.100031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
Three-dimensional particle tracking is a routine experimental procedure for various biophysical applications including magnetic tweezers. A common method for tracking the axial position of particles involves the analysis of diffraction rings whose pattern depends sensitively on the axial position of the bead relative to the focal plane. To infer the axial position, the observed rings are compared with reference images of a bead at known axial positions. Often the precision or accuracy of these algorithms is measured on immobilized beads over a limited axial range, while many experiments are performed using freely mobile beads. This inconsistency raises the possibility of incorrect estimates of experimental uncertainty. By manipulating magnetic beads in a bidirectional magnetic tweezer setup, we evaluated the error associated with tracking mobile magnetic beads and found that the error of tracking a moving magnetic bead increases by almost an order of magnitude compared to the error of tracking a stationary bead. We found that this additional error can be ameliorated by excluding the center-most region of the diffraction ring pattern from tracking analysis. Evaluation of the limitations of a tracking algorithm is essential for understanding the error associated with a measurement. These findings promise to bring increased resolution to three-dimensional bead tracking of magnetic microspheres.
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Affiliation(s)
- Laura A. Carlucci
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Wendy E. Thomas
- Department of Bioengineering, University of Washington, Seattle, Washington
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Piccolo JG, Méndez Harper J, McCalla D, Xu W, Miller S, Doan J, Kovari D, Dunlap D, Finzi L. Force spectroscopy with electromagnetic tweezers. JOURNAL OF APPLIED PHYSICS 2021; 130:134702. [PMID: 38681504 PMCID: PMC11055633 DOI: 10.1063/5.0060276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/07/2021] [Indexed: 05/01/2024]
Abstract
Force spectroscopy using magnetic tweezers (MTs) is a powerful method to probe the physical characteristics of single polymers. Typically, molecules are functionalized for specific attachment to a glass surface at one end and a micrometer-scale paramagnetic bead at the other end. By applying an external magnetic field, multiple molecules can be stretched and twisted simultaneously without exposure to potentially damaging radiation. The majority of MTs utilize mobile, permanent magnets to produce forces on the beads (and the molecule under test). However, translating and rotating the permanent magnets may require expensive precision actuators, limit the rate at which force can be changed, and may induce vibrations that disturb tether dynamics and bead tracking. Alternatively, the magnetic field can be produced with an electromagnet, which allows fast force modulation and eliminates motor-associated vibration. Here, we describe a low-cost quadrapolar electromagnetic tweezer design capable of manipulating DNA-tethered MyOne paramagnetic beads with forces as high as 15 pN. The solid-state nature of the generated B-field modulated along two axes is convenient for accessing the range of forces and torques relevant for studying the activity of DNA motor enzymes like polymerases and helicases. Our design specifically leverages technology available at an increasing number of university maker spaces and student-run machine shops. Thus, it is an accessible tool for undergraduate education that is applicable to a wide range of biophysical research questions.
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Affiliation(s)
- Joseph G. Piccolo
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Joshua Méndez Harper
- Department of Earth Science, University of Oregon, 1272 University of Oregon, Eugene, Oregon 97403, USA
| | - Derrica McCalla
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Wenxuan Xu
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Sam Miller
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Jessie Doan
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Dan Kovari
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - David Dunlap
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
| | - Laura Finzi
- Department of Physics, Emory University, 400 Dowman Dr., Atlanta, Georgia 30322, USA
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Kashkanova AD, Shkarin AB, Mahmoodabadi RG, Blessing M, Tuna Y, Gemeinhardt A, Sandoghdar V. Precision single-particle localization using radial variance transform. OPTICS EXPRESS 2021; 29:11070-11083. [PMID: 33820226 DOI: 10.1364/oe.420670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
We introduce an image transform designed to highlight features with high degree of radial symmetry for identification and subpixel localization of particles in microscopy images. The transform is based on analyzing pixel value variations in radial and angular directions. We compare the subpixel localization performance of this algorithm to other common methods based on radial or mirror symmetry (such as fast radial symmetry transform, orientation alignment transform, XCorr, and quadrant interpolation), using both synthetic and experimentally obtained data. We find that in all cases it achieves the same or lower localization error, frequently reaching the theoretical limit.
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