Thursday, August 29, 2013

Polymerase manager protein UmuD directly regulates Escherichia coli DNA polymerase III α binding to ssDNA

Kathy R. Chaurasiya, Clarissa Ruslie, Michelle C. Silva, Lukas Voortman, Philip Nevin, Samer Lone, Penny J. Beuning and Mark C. Williams

Replication by Escherichia coli DNA polymerase III is disrupted on encountering DNA damage. Consequently, specialized Y-family DNA polymerases are used to bypass DNA damage. The protein UmuD is extensively involved in modulating cellular responses to DNA damage and may play a role in DNA polymerase exchange for damage tolerance. In the absence of DNA, UmuD interacts with the α subunit of DNA polymerase III at two distinct binding sites, one of which is adjacent to the single-stranded DNA-binding site of α. Here, we use single molecule DNA stretching experiments to demonstrate that UmuD specifically inhibits binding of α to ssDNA. We predict using molecular modeling that UmuD residues D91 and G92 are involved in this interaction and demonstrate that mutation of these residues disrupts the interaction. Our results suggest that competition between UmuD and ssDNA for α binding is a new mechanism for polymerase exchange.


Generation of an array of optical bottle beams using a superposition of Bessel beams

A. P. Porfirev and R. V. Skidanov

A procedure for computing the phase transmission function of diffractive optical elements intended to form an array of optical bottle beams is proposed and studied. The procedure is based on a superposition of Bessel beams. We show that the hollow circular beams (optical bottle beams) are suited for trapping transparent spherical micro-objects matched in radius with the beam radius. A series of experiments on trapping transparent micro-objects in the optical bottle arrays is described. Results of an experiment on trapping opaque spherical microparticles in a double optical bottle are reported.


Decomposition of the total momentum in a linear dielectric into field and matter components

Michael E. Crenshaw

The long-standing resolution of the Abraham–Minkowski electromagnetic momentum controversy is predicated on a decomposition of the total momentum of a closed continuum electrodynamic system into separate field and matter components. Using a microscopic model of a simple linear dielectric, we derive Lagrangian equations of motion for the electric dipoles and show that the dielectric can be treated as a collection of stationary simple harmonic oscillators that are driven by the electric field and produce a polarization field in response. The macroscopic energy and momentum are defined in terms of the electric, magnetic, and polarization fields that travel through the dielectric together as a pulse of electromagnetic radiation. We conclude that both the macroscopic total energy and the macroscopic total momentum are entirely electromagnetic in nature for a simple linear dielectric in the absence of significant reflections.


Microrheological Characterization of Collagen Systems: From Molecular Solutions to Fibrillar Gels

Marjan Shayegan, Nancy R. Forde

Collagen is the most abundant protein in the extracellular matrix (ECM), where its structural organization conveys mechanical information to cells. Using optical-tweezers-based microrheology, we investigated mechanical properties both of collagen molecules at a range of concentrations in acidic solution where fibrils cannot form and of gels of collagen fibrils formed at neutral pH, as well as the development of microscale mechanical heterogeneity during the self-assembly process. The frequency scaling of the complex shear modulus even at frequencies of ~10 kHz was not able to resolve the flexibility of collagen molecules in acidic solution. In these solutions, molecular interactions cause significant transient elasticity, as we observed for 5 mg/ml solutions at frequencies above ~200 Hz. We found the viscoelasticity of solutions of collagen molecules to be spatially homogeneous, in sharp contrast to the heterogeneity of self-assembled fibrillar collagen systems, whose elasticity varied by more than an order of magnitude and in power-law behavior at different locations within the sample. By probing changes in the complex shear modulus over 100-minute timescales as collagen self-assembled into fibrils, we conclude that microscale heterogeneity appears during early phases of fibrillar growth and continues to develop further during this growth phase. Experiments in which growing fibrils dislodge microspheres from an optical trap suggest that fibril growth is a force-generating process. These data contribute to understanding how heterogeneities develop during self-assembly, which in turn can help synthesis of new materials for cellular engineering.


Observing single protein binding by optical transmission through a double nanohole aperture in a metal film

Ahmed A. Al Balushi, Ana Zehtabi-Oskuie, and Reuven Gordon

We experimentally demonstrate protein binding at the single particle level. A double nanohole (DNH) optical trap was used to hold onto a 20 nm biotin-coated polystyrene (PS) particle which subsequently is bound to streptavidin. Biotin-streptavidin binding has been detected by an increase in the optical transmission through the DNH. Similar optical transmission behavior was not observed when streptavidin binding sites where blocked by mixing streptavidin with excess biotin. Furthermore, interaction of non-functionalized PS particles with streptavidin did not induce a change in the optical transmission through the DNH. These results are promising as the DNH trap can make an excellent single molecule resolution sensor which would enable studying biomolecular interactions and dynamics at a single particle/molecule level.


Deflection and trapping of spatial solitons in linear photonic potentials

Chandroth P. Jisha, Alessandro Alberucci, Ray-Kuang Lee, and Gaetano Assanto

We investigate the dynamics of spatial optical solitons launched in a medium with a finite perturbation of the refractive index. For longitudinally short perturbations of super-Gaussian transverse profile, as the input power varies we observe a transition from a wave-like behavior where solitons break up into multiple fringes to a particle-like behavior where solitons acquire a transverse velocity retaining their shape. For longitudinally long perturbations with an attractive potential solitons get trapped inside the well and propagate with transverse periodic oscillations, resulting in an efficient power-dependent angular steering or deflection. Using the Ehrenfest theorem we derive analytical expressions for soliton trajectory, and achieve excellent agreement between theory and numerical simulations for large powers, that is, narrow solitons.


Polariton condensation in an optically induced two-dimensional potential

A. Askitopoulos, H. Ohadi, A. V. Kavokin, Z. Hatzopoulos, P. G. Savvidis, and P. G. Lagoudakis

We demonstrate experimentally the condensation of exciton polaritons through optical trapping. The nonresonant pump profile is shaped into a ring and projected to a high quality factor microcavity where it forms a two-dimensional repulsive optical potential originating from the interactions of polaritons with the excitonic reservoir. Increasing the population of particles in the trap eventually leads to the emergence of a confined polariton condensate that is spatially decoupled from the decoherence inducing reservoir, before any buildup of coherence on the excitation region. In a reference experiment, where the trapping mechanism is switched off by changing the excitation intensity profile, polariton condensation takes place for excitation densities more than two times higher and the resulting condensate is subject to much stronger dephasing and depletion processes.