Monday, October 20, 2014

A biomechanical mechanism for initiating DNA packaging

Haowei Wang, Samuel Yehoshua, Sabrina S. Ali, William Wiley Navarre and Joshua N. Milstein

The bacterial chromosome is under varying levels of mechanical stress due to a high degree of crowding and dynamic protein–DNA interactions experienced within the nucleoid. DNA tension is difficult to measure in cells and its functional significance remains unclear although in vitro experiments have implicated a range of biomechanical phenomena. Using single-molecule tools, we have uncovered a novel protein–DNA interaction that responds to fluctuations in mechanical tension by condensing DNA. We combined tethered particle motion (TPM) and optical tweezers experiments to probe the effects of tension on DNA in the presence of the Hha/H-NS complex. The nucleoid structuring protein H-NS is a key regulator of DNA condensation and gene expression in enterobacteria and its activity in vivo is affected by the accessory factor Hha. We find that tension, induced by optical tweezers, causes the rapid compaction of DNA in the presence of the Hha/H-NS complex, but not in the presence of H-NS alone. Our results imply that H-NS requires Hha to condense bacterial DNA and that this condensation could be triggered by the level of mechanical tension experienced along different regions of the chromosome.


Decoupled and simultaneous three-dimensional imaging and optical manipulation through a single objective

Arran Curran, Simon Tuohy, Dirk G. A. L. Aarts, Martin J. Booth, Tony Wilson, and Roel P. A. Dullens

The combination of optical manipulation and three-dimensional imaging is a central technique in fields ranging from medicine to physics. Using the objective lens simultaneously for optical trapping and imaging, however, inherently confines the trapping and imaging planes to the same focal plane. Here, we combine remote refocusing microscopy and optical trapping to optically decouple the imaging and trapping planes, achieving aberration-free three-dimensional imaging and simultaneous, decoupled optical trapping without the need for feedback or aberration corrections. We demonstrate our approach by directly imaging the flow field around optically trapped spheres in three dimensions. Due to its compatibility with other imaging and optical manipulation techniques, our approach is relevant to the wide range of fields that combine imaging and optical manipulation, such as physical chemistry, cell biology, and soft matter.


Friday, October 17, 2014

Beam configuration proposal to verify that scattering forces come from the orbital part of the Poynting vector

Manuel I. Marqués
In this Letter, the optical forces on an electric dipole generated by a beam made up of two circularly polarized Hermite–Gaussian modes have been analyzed. When the intensity of the two modes is not the same, the mechanical action of the scattering force is completely different from the behavior of the Poynting vector. The dynamics of resonant metallic nanoparticles under this field have been calculated by means of Langevin molecular dynamic simulations. This configuration could be useful to experimentally verify how radiation pressure on a Rayleigh particle is due to the transfer of linear momentum coming solely from the orbital part of the Poynting vector.


Microspherical photonics: Sorting resonant photonic atoms by using light

Alexey V. Maslov and Vasily N. Astratov

A method of sorting microspheres by resonant light forces in vacuum, air, or liquid is proposed. Based on a two-dimensional model, it is shown that the sorting can be realized by allowing spherical particles to traverse a focused beam. Under resonance with the whispering gallery modes, the particles acquire significant velocity along the beam direction. This opens a unique way of large-volume sorting of nearly identical photonic atoms with 1/Q accuracy, where Q is the resonance quality factor. This is an enabling technology for developing super-low-loss coupled-cavity structures and devices.


Wednesday, October 15, 2014

How to calibrate an object-adapted optical trap for force sensing and interferometric shape tracking of asymmetric structures

Matthias Koch and Alexander Rohrbach

Optical traps have shown to be a flexible and powerful tool for 3D manipulations on the microscale. However, when it comes to sensitive measurements of particle displacements and forces thorough calibration procedures are required, which can be already demanding for trapped spheres. For asymmetric structures, with more complicated shapes, such as helical bacteria, novel calibration schemes need to be established. The paper describes different methods of how to extract various calibration parameters of a tiny helical bacterium, which is trapped and tracked in shape by scanning line optical tweezers. Tiny phase differences of the light scattered at each slope of the bacterium are measured by back focal plane interferometry, providing precise and high bandwidth information about fast deformations of the bacterium. A simplified theoretical model to estimate the optical forces on a chain like structure is presented. The methods presented here should be of interest to people that investigate optical trapping and tracking of asymmetric particles.


Tuesday, October 14, 2014

Trapping particles using waveguide-coupled gold bowtie plasmonic tweezers

Pin-Tso Lin, Heng-Yi Chu, Tsan-Wen Lu and Po-Tsung Lee

We propose and demonstrate a trapping configuration integrating coupled waveguides and gold bowtie structures to form near-field plasmonic tweezers. Compared with excitation from the top, waves coupled through the waveguide can excite specific bowties on the waveguide and trap particles precisely. Thus this scheme is more efficient and compact, and will assist the circuit design on a chip. With lightning rod and gap effects, the gold bowtie structures can generate highly concentrated resonant fields and induce trapping forces as strong as 652 pN W−1 on particles with diameters as small as 20 nm. This trapping capability is investigated numerically and verified experimentally with observations of the transport, trapping, and release of particles in the system.


Site Specific Supramolecular Heterogeneous Catalysis by Optically Patterned Soft Oxometalate - Porous Organic Framework (SOM-POF) Hybrid on a Chip

Preethi Thomas, Cuiying Pei, Basudev Roy, Subhrokoli Ghosh, Santu Das, Ayan Banerjee, Teng Ben, Shilun Qiu and Soumyajit Roy
We have designed a supramolecularly bound multi-component catalytic material based on a soft oxometalate (SOM) and a porous organic framework (POF) material which shows high catalytic conversion efficiency. We have also used this material for site directed supramolecular heterogeneous catalysis with yield even higher than in the bulk, and with micron-level precision by controllably depositing the material on a glass substrate, making a reactor chip, using a thermo-optical tweezers. Various SOM-POF composites have been prepared in dispersion phase and patterned using thermo-optic tweezers and their catalytic activities have been compared with a benchmark molecular catalyst [PMo12]. This work can lead to further explorations for hybrid materials formed out of well defined molecular level precursors which can be controllably micro-patterned in order to catalyze targeted reactions simultaneously.


Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex

Ali A. Almaqwashi, Thayaparan Paramanathan, Per Lincoln, Ioulia Rouzina, Fredrik Westerlund and Mark C. Williams

DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ‐bidppz‐(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.