Ana Lisica, Stephan W. Grill
Transcription is the first step in the expression of genetic information and it is carried out by large macromolecular enzymes called RNA polymerases. Transcription has been studied for many years and with a myriad of experimental techniques, ranging from bulk studies to high-resolution transcript sequencing. In this review, we emphasise the advantages of using single-molecule techniques, particularly optical tweezers, to study transcription dynamics. We give an overview of the latest results in the single-molecule transcription field, focusing on transcription by eukaryotic RNA polymerases. Finally, we evaluate recent quantitative models that describe the biophysics of RNA polymerase translocation and backtracking dynamics.
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Jiafang Li, Jing Liu, Ximin Tian, Zhi-Yuan Li
Metal nanoparticles have unique localized surface plasmon resonance (SPR) properties due to the strong interaction of localized surface plasmon polariton (SPP) with incident light. This review will cover some of our recent theoretical and experimental studies on exploring the unique optical interaction and mechanical motion properties of plasmonic particles that originate from SPR enhanced light-matter interaction. Firstly, the efficient enhancement of both the fluorescence excitation and emission process of dye molecules by the double SPR modes (longitudinal and transverse modes) in gold nanorods, and surface plasmon amplification in metal nanoparticles with gain is discussed. Secondly, it is theoretically demonstrated that two basic physical processes of molecules interacting with light, i.e., the elastic Rayleigh scattering and inelastic Raman scattering, will strongly intertwine and correlate with each other in many plasmonic surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering (TERS) nanosystems. Thirdly, it is experimentally shown that SPR can enhance the optical force and torque of nanoparticles embedded within non-intrusive optical tweezers. The work presented in this review shows that plasmonic particles can possess unique optical interaction and mechanical motion properties when their geometries are deliberately controlled.
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Gregor Posnjak, Simon Čopar & Igor Muševič
Topology has an increasingly important role in the physics of condensed matter, quantum systems, material science, photonics and biology, with spectacular realizations of topological concepts in liquid crystals. Here we report on long-lived hidden topological states in thermally quenched, chiral nematic droplets, formed from string-like, triangular and polyhedral constellations of monovalent and polyvalent singular point defects. These topological defects are regularly packed into a spherical liquid volume and stabilized by the elastic energy barrier due to the helical structure and confinement of the liquid crystal in the micro-sphere. We observe, for the first time, topological three-dimensional point defects of the quantized hedgehog charge q=−2, −3. These higher-charge defects act as ideal polyvalent artificial atoms, binding the defects into polyhedral constellations representing topological molecules.
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Frederic Català, Ferran Marsà, Mario Montes-Usategui, Arnau Farré & Estela Martín-Badosa
Optical trapping has become an optimal choice for biological research at the microscale due to its non-invasive performance and accessibility for quantitative studies, especially on the forces involved in biological processes. However, reliable force measurements depend on the calibration of the optical traps, which is different for each experiment and hence requires high control of the local variables, especially of the trapped object geometry. Many biological samples have an elongated, rod-like shape, such as chromosomes, intracellular organelles (e.g., peroxisomes), membrane tubules, certain microalgae, and a wide variety of bacteria and parasites. This type of samples often requires several optical traps to stabilize and orient them in the correct spatial direction, making it more difficult to determine the total force applied. Here, we manipulate glass microcylinders with holographic optical tweezers and show the accurate measurement of drag forces by calibration-free direct detection of beam momentum. The agreement between our results and slender-body hydrodynamic theoretical calculations indicates potential for this force-sensing method in studying protracted, rod-shaped specimens.
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Hongchang Deng, Yaxun Zhang, Tinging Yuan, Xiaotong Zhang, Yu Zhang, Zhihai Liu, and Libo Yuan
We proposed and fabricated a fiber-based optical gun for both particle trapping and shooting. The all-fiber device is made of a coaxial core optical fiber with a center core and a coaxial circular core. The fiber has a cone-frustum-shaped tip to enable the circular core to generate a focused ring light as a trapping beam, providing a stable 3D trapping potential well. When a small particle is trapped, a Gaussian beam is launched as a shooting light at the fiber center core to push the particle away from the fiber tip along the propagation direction of the beam. Here, we find that (1) the highly focused ring field with considerably lowered focusing intensity can generate a very stable particle-trapping potential well in three dimensions and the photothermal effect is also greatly reduced due to the lower optical power requirement for trapping and (2) the shooting light with a Gaussian profile not only supplies a radiation pushing force on the small particle, but also has restrictions and guiding effects as a gun barrel to propel the small particle out of the trapping well at a high speed along the beam propagation direction. The particle shooting distance can reach several hundreds of micrometers. Transverse deviation from the optical axis can be controlled within several micrometers under disturbances of ambient fluid flow. Our proposed method extends the potential applications of fiber-based optical manipulation, e.g., microparticle sorting in biology, accurate delivery of microparticles of a drug to the target cells, and observation of drug synergism.
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Tetsuhiro Kudo, Hajime Ishihara, and Hiroshi Masuhara
We demonstrate resonance optical trapping of individual dye-doped polystyrene particles with blue- and red-detuned lasers whose energy are higher and lower compared to electronic transition of the dye molecules, respectively. Through the measurement on how long individual particles are trapped at the focus, we here show that immobilization time of dye-doped particles becomes longer than that of bare ones. We directly confirm that the immobilization time of dye-doped particles trapped by the blue-detuned laser becomes longer than that by the red-detuned one. These findings are well interpreted by our previous theoretical proposal based on nonlinear optical response under intense laser field. It is discussed that the present result is an important step toward efficient and selective manipulation of molecules, quantum dots, nanoparticles, and various nanomaterials based on their quantum mechanical properties.
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Joshua Lamstein, Anna Bezryadina, Daryl Preece, Joseph C. Chen, and Zhigang Chen
We design and demonstrate new types of optical tweezers with lateral pulling forces that allow full control of biological samples with complex geometric shapes. With appropriate beam shaping, the dual tug-of-war tweezers effectively hold and stretch elongated biological objects of different sizes, and the triangular tug-of-war tweezers with threefold rotational symmetry steadily hold asymmetric objects in the plane of observation and exert stretching forces along three directions. We successfully apply these tweezers to manipulate microparticles and bacterial cells in aqueous media.
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Kristin E Haugstad, Soosan Hadjialirezaei, Bjørn T Stokke, C Fred Brewer, Thomas A Gerken, Joy Burchell, Gianfranco Picco, Marit Sletmoen
The molecular mechanism(s) underlying the enhanced self-interactions of mucins possessing the Tn (GalNAcα1-Ser/Thr) or STn (NeuNAcα2-6GalNAcα1-Ser/Thr) cancer markers were investigated using optical tweezers (OT). The mucins examined included modified porcine submaxillary mucin containing the Tn epitope (Tn-PSM), ovine submaxillary mucin with the STn epitope (STn-OSM), and recombinant MUC1 analogs with either the Tn and STn epitope. OT experiments in which the mucins were immobilized onto polystyrene beads revealed identical self-interaction characteristics for all mucins. Identical binding strength and energy landscape characteristics were also observed for synthetic polymers displaying multiple GalNAc decorations. Polystyrene beads without immobilized mucins showed no self-interactions and also no interactions with mucin-decorated polystyrene beads. Taken together, the experimental data suggest that in these molecules, the GalNAc residue mediates interactions independent of the anchoring polymer backbone. Furthermore, GalNAc–GalNAc interactions appear to be responsible for self-interactions of mucins decorated with the STn epitope. Hence, Tn-MUC1 and STn-MUC1 undergo self-interactions mediated by the GalNAc residue in both epitopes, suggesting a possible molecular role in cancer. MUC1 possessing the T (Galβ1-3GalNAcα1-Ser/Thr) or ST antigen (NeuNAcα2-3Galβ1-3GalNAcα1-Ser/Thr) failed to show self-interactions. However, in the case of ST-MUC1, self-interactions were observed after subsequent treatment with neuraminidase and β-galactosidase. This enzymatic treatment is expected to introduce Tn-epitopes and these observations thus further strengthen the conclusion that the observed interactions are mediated by the GalNAc groups.
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Nicola A. Nodargi, Paolo Bisegna, Federica Caselli
Due to its crucial role in pathophysiology, erythrocyte deformability represents a subject of intense experimental and modeling research. Here a computational approach to electro-deformation for erythrocyte mechanical characterization is presented. Strong points of the proposed strategy are: (1) an accurate computation of the mechanical actions induced on the cell by the electric field, (2) a microstructurally-based continuum model of the erythrocyte mechanical behavior, (3) an original rotation-free shell finite element, especially suited to the application in hand. As proved by the numerical results, the developed tool is effective and sound, and can foster the role of electro-deformation in single-cell mechanical phenotyping.
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Claudia T. Mierke, Tony Fischer, Stefanie Puder, Tom Kunschmann, Birga Soetje & Wolfgang H. Ziegler
The focal adhesion kinase (FAK) regulates the dynamics of integrin-based cell adhesions important for motility. FAK’s activity regulation is involved in stress-sensing and focal-adhesion turnover. The effect of FAK on 3D migration and cellular mechanics is unclear. We analyzed FAK knock-out mouse embryonic fibroblasts and cells expressing a kinase-dead FAK mutant, R454-FAK, in comparison to FAK wild-type cells. FAK knock-out and FAKR454/R454 cells invade dense 3D matrices less efficiently. These results are supported by FAK knock-down in wild-type fibroblasts and MDA-MB-231 human breast cancer cells showing reduced invasiveness. Pharmacological interventions indicate that in 3D matrices, cells deficient in FAK or kinase-activity behave similarly to wild-type cells treated with inhibitors of Src-activity or actomyosin-contractility. Using magnetic tweezers experiments, FAKR454/R454 cells are shown to be softer and exhibit impaired adhesion to fibronectin and collagen, which is consistent with their reduced 3D invasiveness. In line with this, FAKR454/R454 cells cannot contract the matrix in contrast to FAK wild-type cells. Finally, our findings demonstrate that active FAK facilitates 3D matrix invasion through increased cellular stiffness and transmission of actomyosin-dependent contractile force in dense 3D extracellular matrices.
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