Wednesday, September 28, 2016

Elastic Properties of Nucleic Acids by Single-Molecule Force Spectroscopy

Joan Camunas-Soler, Marco Ribezzi-Crivellari, and Felix Ritort

We review the current knowledge on the use of single-molecule force spectroscopy techniques to extrapolate the elastic properties of nucleic acids. We emphasize the lesser-known elastic properties of single-stranded DNA. We discuss the importance of accurately determining the elastic response in pulling experiments, and we review the simplest models used to rationalize the experimental data as well as the experimental approaches used to pull single-stranded DNA. Applications used to investigate DNA conformational transitions and secondary structure formation are also highlighted. Finally, we provide an overview of the effects of salt and temperature and briefly discuss the effects of contour length and sequence dependence.


Erythrocytes and their role as health indicator: Using structure in a patient-orientated precision medicine approach

Etheresia Pretorius, Oore-ofe O. Olumuyiwa-Akeredolu, Sthembile Mbotwe, Janette Bester

The relevance of erythrocyte light microscopy analysis (a well-known haematological method) is under the spotlight, however there is a place for innovative electron microscopy, (together with biochemical markers) in a pathology laboratory. Inflammation is a key indicator of the health status and erythrocytes are extremely sensitive to oxidative stress or cytokine upregulation, which typically accompany systemic inflammation in most diseases. They are probably the most adaptable cells, and due to their short lifespan, may form a vital indicator of health, and could play a central part in tracking disease and treatment. As the NIH is proposing a precision medicine approach and because individualised medicine should form an essential part in diagnosis and treatment, biophysical combined with biochemical analysis of erythrocytes may be a novel method to track the inflammatory status before and after treatment. This will allow a fully individualised patient orientated precision medicine approach, where one-medication-regime-fits-all is no longer appropriate.


Autoenhanced Raman Spectroscopy via Plasmonic Trapping for Molecular Sensing

Soonwoo Hong, On Shim, Hyosung Kwon, and Yeonho Choi

As a label-free and sensitive biosensor, surface-enhanced Raman spectroscopy (SERS) is a rapidly emerging technique. However, because SERS spectra are obtained in the area of light excitation and the enhancement effect can be varied depending on the position of a substrate, it is important to match the enhanced area with an illuminated spot. Here, in order to overcome such difficulty, we demonstrated a new technique combining SERS with plasmonic trapping. By plasmonic trapping, we can collect gold nanoparticles (GNPs) in the middle of initially fabricated nanobowtie structures where a laser is excited. As a result of trapping GNPs, hot-spots are formed at that area. Because SERS is measured in the area irradiated by a laser, hot-spot can be simultaneously coincided with a detection site for SERS. By using this, we detected Rhodamine 6G to 100 pM. To further verify and improve the reproducibility of our technique, we also calculated the electric field distribution, trapping force and trapping potential.


Negative optical spin torque wrench of a non-diffracting non-paraxial fractional Bessel vortex beam

F.G. Mitri

An absorptive Rayleigh dielectric sphere in a non-diffracting non-paraxial fractional Bessel vortex beam experiences a spin torque. The axial and transverse radiation spin torque components are evaluated in the dipole approximation using the radiative correction of the electric field. Particular emphasis is given on the polarization as well as changing the topological charge α and the half-cone angle of the beam. When α is zero, the axial spin torque component vanishes. However, when α becomes a real positive number, the vortex beam induces left-handed (negative) axial spin torque as the sphere shifts off-axially from the center of the beam. The results show that a non-diffracting non-paraxial fractional Bessel vortex beam is capable of inducing a spin reversal of an absorptive Rayleigh sphere placed arbitrarily in its path. Potential applications are yet to be explored in particle manipulation, rotation in optical tweezers, optical tractor beams, and the design of optically-engineered metamaterials to name a few areas.


Tuesday, September 27, 2016

Identification of volume phase transition of a single microgel particle using optical tweezers

D Karthickeyan, Deepak K Gupta and B V R Tata

Poly (N-isopropyl acrylamide-co-acrylic acid) (PNIPAM-co-Aac) microgel particles are pH responsive and exhibit volume phase transition (VPT) upon variation of pH. Dynamic light scattering (DLS) is used conventionally to identify VPT and requires a dilute suspension with particle concentration ~107 particles cm−3 and if particles are polydisperse in nature, DLS data interpretation is relatively difficult. Here we show that optical tweezers allow one to measure the VPT of a single microgel particle by measuring the optical trap stiffness, κ of trapped particle as a function of pH. We report here a sudden change in κ at VPT, which is shown to arise from a sudden decrease in particle diameter with a concomitant increase in the refractive index of the particle at VPT.


Stable, Free-space Optical Trapping and Manipulation of Sub-micron Particles in an Integrated Microfluidic Chip

Jisu Kim & Jung H. Shin

We demonstrate stable, free-space optical trapping and manipulation in an integrated microfluidic chip using counter-propagating beams. An inverted ridge-type waveguide made of SU8 is cut across by an open trench. The design of the waveguide provides low propagation losses and small divergence of the trapping beam upon emergence from the facet, and the trench designed to be deeper and wider than the optical mode enables full utilization of the optical power with an automatic alignment for counter-propagating beams in a trap volume away from all surfaces. After integration with polydimethylsiloxane (PDMS) microfluidic channel for particle delivery, 0.65 μm and 1 μm diameter polystyrene beads were trapped in free space in the trench, and manipulated to an arbitrary position between the waveguides with a resolution of < 100 nm. Comparison with numerical simulations confirm stable trapping of sub-micron particles, with a 10 kBT threshold power of less than 1 mW and a stiffness that can be 1 order of magnitude larger than that of comparable fiber-based trapping methods.


Single-molecule dissection of stacking forces in DNA

Fabian Kilchherr, Christian Wachauf, Benjamin Pelz, Matthias Rief, Martin Zacharias, Hendrik Dietz

We directly measured at the single-molecule level the forces and lifetimes of DNA base-pair stacking interactions for all stack sequence combinations. Our experimental approach combined dual-beam optical tweezers with DNA origami components to allow positioning of blunt-end DNA helices so that the weak stacking force could be isolated. Base-pair stack arrays that lacked a covalent backbone connection spontaneously dissociated at average rates ranging from 0.02 to 500 per second, depending on the sequence combination and stack array size. Forces in the range from 2 to 8 piconewtons that act along the helical direction only mildly accelerated the stochastic unstacking process. The free-energy increments per stack that we estimate from the measured forward and backward kinetic rates ranged from –0.8 to –3.4 kilocalories per mole, depending on the sequence combination. Our data contributes to understanding the mechanics of DNA processing in biology, and it is helpful for designing the kinetics of DNA-based nanoscale devices according to user specifications.


Coupling rotational and translational motion via a continuous measurement in an optomechanical sphere

Jason F. Ralph, Kurt Jacobs, and Jonathon Coleman

We consider a measurement of the position of a spot painted on the surface of a trapped nano-optomechanical sphere. The measurement extracts information about the position of the spot and in doing so measures a combination of the orientation and position of the sphere. The quantum backaction of the measurement entangles and correlates these two degrees of freedom. Such a measurement is not available for atoms or ions and provides a mechanism to probe the quantum mechanical properties of trapped optomechanical spheres. In performing simulations of this measurement process we also test a numerical method introduced recently by Rouchon and collaborators [H. Amini, M. Mirrahimi, and P. Rouchon, in Proceedings of the 50th IEEE Conference on Decision and Control (CDC, 2011), pp. 6242–6247; P. Rouchon and J. F. Ralph, Phys. Rev. A 91, 012118 (2015)] for solving stochastic master equations. This method guarantees the positivity of the density matrix when the Lindblad operators for all simultaneous continuous measurements are mutually commuting. We show that it is both simpler and far more efficient than previous methods.


Fabrication of quartz microcylinders by laser interference lithography for angular optical tweezers

Zhanna Santybayeva ; Afaf Meghit ; Rudy Desgarceaux ; Roland Teissier ; Frederic Pichot ; Charles de Marin ; Benoit Charlot ; Francesco Pedaci

The use of optical tweezers (OTs) and spin angular momentum transfer to birefringent particles allows new mechanical measurements in systems where torque and rotation are relevant parameters at the single-molecule level. There is a growing interest in developing simple, fast, and inexpensive protocols to produce a large number of submicron scale cylinders of quartz, a positive uniaxial birefringent crystal, to be employed for such angular measurements in OTs. Here, we show that laser interference lithography, a method well known for its simplicity, fulfills these requirements and produces quartz cylindrical particles that we successfully use to apply and measure optical torque in the piconewton nm range in an optical torque wrench.


Friday, September 23, 2016

Fibrin Networks Support Recurring Mechanical Loads by Adapting their Structure across Multiple Scales

Nicholas A. Kurniawan, Bart E. Vos, Andreas Biebricher, Gijs J.L. Wuite, Erwin J.G. Peterman, Gijsje H. Koenderink

Tissues and cells sustain recurring mechanical loads that span a wide range of loading amplitudes and timescales as a consequence of exposure to blood flow, muscle activity, and external impact. Both tissues and cells derive their mechanical strength from fibrous protein scaffolds, which typically have a complex hierarchical structure. In this study, we focus on a prototypical hierarchical biomaterial, fibrin, which is one of the most resilient naturally occurring biopolymers and forms the structural scaffold of blood clots. We show how fibrous networks composed of fibrin utilize irreversible changes in their hierarchical structure at different scales to maintain reversible stress stiffening up to large strains. To trace the origin of this paradoxical resilience, we systematically tuned the microstructural parameters of fibrin and used a combination of optical tweezers and fluorescence microscopy to measure the interactions of single fibrin fibers for the first time, to our knowledge. We demonstrate that fibrin networks adapt to moderate strains by remodeling at the network scale through the spontaneous formation of new bonds between fibers, whereas they adapt to high strains by plastic remodeling of the fibers themselves. This multiscale adaptation mechanism endows fibrin gels with the remarkable ability to sustain recurring loads due to shear flows and wound stretching. Our findings therefore reveal a microscopic mechanism by which tissues and cells can balance elastic nonlinearity and plasticity, and thus can provide microstructural insights into cell-driven remodeling of tissues.