Tuesday, June 27, 2017

Metasurfaces and Colloidal Suspensions Composed of 3D Chiral Si Nanoresonators

Ruggero Verre, Lei Shao, Nils Odebo Länk, Pawel Karpinski, Andrew B. Yankovich, Tomasz J. Antosiewicz, Eva Olsson, Mikael Käll
High-refractive-index silicon nanoresonators are promising low-loss alternatives to plasmonic particles in CMOS-compatible nanophotonics applications. However, complex 3D particle morphologies are challenging to realize in practice, thus limiting the range of achievable optical functionalities. Using 3D film structuring and a novel gradient mask transfer technique, the first intrinsically chiral dielectric metasurface is fabricated in the form of a monolayer of twisted silicon nanocrescents that can be easily detached and dissolved into colloidal suspension. The metasurfaces exhibit selective handedness and a circular dichroism as large as 160° µm−1 due to pronounced differences in induced current loops for left-handed and right-handed polarization. The detailed morphology of the detached particles is analyzed using high-resolution transmission electron microscopy. Furthermore, it is shown that the particles can be manipulated in solution using optical tweezers. The fabrication and detachment method can be extended to different nanoparticle geometries and paves the way for a wide range of novel nanophotonic experiments and applications of high-index dielectrics.


Biolens behavior of RBCs under optically-induced mechanical stress

Francesco Merola, Álvaro Barroso, Lisa Miccio, Pasquale Memmolo, Martina Mugnano, Pietro Ferraro, Cornelia Denz

In this work, the optical behavior of Red Blood Cells (RBCs) under an optically-induced mechanical stress was studied. Exploiting the new findings concerning the optical lens-like behavior of RBCs, the variations of the wavefront refracted by optically-deformed RBCs were further investigated. Experimental analysis have been performed through the combination of digital holography and numerical analysis based on Zernike polynomials, while the biological lens is deformed under the action of multiple dynamic optical tweezers. Detailed wavefront analysis provides comprehensive information about the aberrations induced by the applied mechanical stress. By this approach it was shown that the optical properties of RBCs in their discocyte form can be affected in a different way depending on the geometry of the deformation. In analogy to classical optical testing procedures, optical parameters can be correlated to a particular mechanical deformation. This could open new routes for analyzing cell elasticity by examining optical parameters instead of direct but with low resolution strain analysis, thanks to the high sensitivity of the interferometric tool. Future application of this approach could lead to early detection and diagnosis of blood diseases through a single-step wavefront analysis for evaluating different cells elasticity.


β -Cyclodextrin polymer binding to DNA: Modulating the physicochemical parameters

J. C. B. Rocha, E. F. Silva, M. F. Oliveira, F. B. Sousa, A. V. N. C. Teixeira, and M. S. Rocha

Cyclodextrins and cyclodextrins-modified molecules have interesting and appealing properties due to their capacity to host components that are normally insoluble or poorly soluble in water. In this work, we investigate the interaction of a β-cyclodextrin polymer (poly-β-CD) with λ-DNA. The polymers are obtained by the reaction of β-CD with epichlorohydrin in alkaline conditions. We have used optical tweezers to characterize the changes of the mechanical properties of DNA molecules by increasing the concentration of poly-β-CD in the sample. The physical chemistry of the interaction is then deduced from these measurements by using a recently developed quenched-disorder statistical model. It is shown that the contour length of the DNA does not change in the whole range of poly-β-CD concentration (<300μM). On the other hand, significant alterations were observed in the persistence length that identifies two binding modes corresponding to the clustering of ∼2.6 and ∼14 polymer molecules along the DNA double helix, depending on the polymer concentration. Comparing these results with the ones obtained for monomeric β-CD, it was observed that the concentration of CD that alters the DNA persistence length is considerably smaller when in the polymeric form. Also, the binding constant of the polymer-DNA interaction is three orders of magnitude higher than the one found for native (monomeric) β-CD. These results show that the polymerization of the β-CD strongly increases its binding affinity to the DNA molecule. This property can be wisely used to modulate the binding of cyclodextrins to the DNA double helix.


Experimental comparison of forces resisting viral DNA packaging and driving DNA ejection

Nicholas Keller, Zachary T. Berndsen, Paul J. Jardine, and Douglas E. Smith

We compare forces resisting DNA packaging and forces driving DNA ejection in bacteriophage phi29 with theoretical predictions. Ejection of DNA from prohead-motor complexes is triggered by heating complexes after in vitro packaging and force is inferred from the suppression of ejection by applied osmotic pressure. Ejection force from 0% to 80% filling is found to be in quantitative agreement with predictions of a continuum mechanics model that assumes a repulsive DNA-DNA interaction potential based on DNA condensation studies and predicts an inverse-spool conformation. Force resisting DNA packaging from ∼80% to 100% filling inferred from optical tweezers studies is also consistent with the predictions of this model. The striking agreement with these two different measurements suggests that the overall energetics of DNA packaging is well described by the model. However, since electron microscopy studies of phi29 do not reveal a spool conformation, our findings suggest that the spool model overestimates the role of bending rigidity and underestimates the role of intrastrand repulsion. Below ∼80% filling the inferred forces resisting packaging are unexpectedly lower than the inferred ejection forces, suggesting that in this filling range the forces are less accurately determined or strongly temperature dependent.


A unique profilin-actin interface is important for malaria parasite motility

Catherine A. Moreau, Saligram P. Bhargav , Hirdesh Kumar , Katharina A. Quadt , Henni Piirainen, Léanne Strauss, Jessica Kehrer, Martin Streichfuss, Joachim P. Spatz, Rebecca C. Wade, Inari Kursula , Friedrich Frischknecht

Profilin is an actin monomer binding protein that provides ATP-actin for incorporation into actin filaments. In contrast to higher eukaryotic cells with their large filamentous actin structures, apicomplexan parasites typically contain only short and highly dynamic microfilaments. In apicomplexans, profilin appears to be the main monomer-sequestering protein. Compared to classical profilins, apicomplexan profilins contain an additional arm-like β-hairpin motif, which we show here to be critically involved in actin binding. Through comparative analysis using two profilin mutants, we reveal this motif to be implicated in gliding motility of Plasmodium berghei sporozoites, the rapidly migrating forms of a rodent malaria parasite transmitted by mosquitoes. Force measurements on migrating sporozoites and molecular dynamics simulations indicate that the interaction between actin and profilin fine-tunes gliding motility. Our data suggest that evolutionary pressure to achieve efficient high-speed gliding has resulted in a unique profilin-actin interface in these parasites.


Trapping Two Types of Particles Using a Laguerre–Gaussian Correlated Schell-Model Beam

Yuan Zhou; Hua-Feng Xu; Yangsheng Yuan; Ji Peng; Jun Qu; Wei Huang

Based on the Rayleigh scattering theory, the radiation forces and the trap stiffness on Rayleigh dielectric sphere induced by a focused Laguerre-Gaussian correlated Schell-model (LGCSM) beam are theoretically studied. It is found that by choosing the appropriate transverse coherence width, mode orders, transverse beam width, and focus lengths, a Rayleigh particle whose refractive index is larger or smaller than the ambient medium can be trapped. Our results will have some theoretical reference value for optical trapping.

Friday, June 23, 2017

Transition Path Times Measured by Single-Molecule Spectroscopy

Hoi Sung Chung

The transition path is a tiny fraction of a molecular trajectory during which the free-energy barrier is crossed. It is a single-molecule property and contains all mechanistic information of folding processes of biomolecules such as proteins and nucleic acids. However, the transition path has been difficult to probe because it is short and rarely visited when transitions actually occur. Recent technical advances in single-molecule spectroscopy have made it possible to directly probe transition paths, which has opened up new theoretical and experimental approaches to investigating folding mechanisms. This article reviews recent single-molecule fluorescence and force spectroscopic measurements of transition path times and their connection to both theory and simulations.


Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch

My-Tra Le, Wojciech K Kasprzak, Bruce A. Shapiro & Anne E Simon

How plus-strand [+]RNA virus genomes transition from translation templates to replication templates is a matter of much speculation. We have previously proposed that, for Turnip crinkle virus, binding of the encoded RNA-dependent RNA polymerase (RdRp) to the 3′UTR of the [+]RNA template promotes a regional wide-spread conformational switch to an alternative structure that disassembles the cap-independent translation element (CITE) in the 3′UTR. The active 3′CITE folds into a tRNA-like T-shaped structure (TSS) that binds to 80S ribosomes and 60S subunits in the P-site. In this Point-of-View, we discuss the history of our research on the TSS and our recent report combining coarse level single molecule force spectroscopy (optical tweezers) with fine-grain computer simulations of this experimental process and biochemical approaches to obtain a detailed understanding of how RdRp binding in the TSS vicinity might lead to an extensive rearrangement of the RNA structure.


Cooperativity of myosin interaction with thin filaments is enhanced by stabilizing substitutions in tropomyosin

Daniil V. Shchepkin, Salavat R. Nabiev, Galina V. Kopylova, Alexander M. Matyushenko, Dmitrii I. Levitsky, Sergey Y. Bershitsky, Andrey K. Tsaturyan

Muscle contraction is powered by myosin interaction with actin-based thin filaments containing Ca2+-regulatory proteins, tropomyosin and troponin. Coiled-coil tropomyosin molecules form a long helical strand that winds around actin filament and either shields actin from myosin binding or opens it. Non-canonical residues G126 and D137 in the central part of tropomyosin destabilize its coiled-coil structure. Their substitutions for canonical ones, G126R and D137L, increase structural stability and the velocity of sliding of reconstructed thin filaments along myosin coated surface. The effect of these stabilizing mutations on force of the actin–myosin interaction is unknown. It also remains unclear whether the stabilization affects single actin–myosin interactions or it modifies the cooperativity of the binding of myosin molecules to actin. We used an optical trap to measure the effects of the stabilization on step size, unitary force and duration of the interactions at low and high load and compared the results with those obtained in an in vitro motility assay. We found that significant prolongation of lifetime of the actin–myosin complex under high load observed at high extent of tropomyosin stabilization, i.e. with double mutant, G126R/D137L, correlates with higher force in the motility assay. Also, the higher the extent of stabilization of tropomyosin, the fewer myosin molecules are needed to propel the thin filaments. The data suggest that the effects of the stabilizing mutations in tropomyosin on the myosin interaction with regulated thin filaments are mainly realized via cooperative mechanisms by increasing the size of cooperative unit.


Setting up of holographic optical tweezer arrays

Deepak K. Gupta, B. V. R. Tata, and T. R. Ravindran

Optical tweezers use tightly focused laser beams to hold and move microscopic objects in a solvent. However, many applications require simultaneous control over multitude of particles, positioning them in 3D space at desired locations with desired symmetry, which is made possible by the use of holographic optical tweezers using the technique of beam shaping and holography. We have designed and developed a holographic optical tweezer set-up using a phase only liquid crystal, reflective spatial light modulator. We employ the technique of phase modulation to modulate the phase of the beam by generating holograms using Random Superposition (RS) and weighted Gerchberg Saxton algorithm (WGS) algorithm for generating desired patterns of light at the trapping plane. A 4×4 array of beams with square symmetry was generated using WGS algorithm and trapped polystyrene particles of size 1.2 micron in a 4×4 two dimensional array. There were uniformity issues among the trap intensities, as we move away from the zeroth order spot. This was corrected by taking into account diffraction effects due to the pixelated nature of SLM modulating the intensity of the trap spots and the ghost order suppression by spatial disorder.