Optical Trapping Experiments Research Articles

Gold nanoparticles: enhanced optical trapping and sensitivity coupled with significant heating

Gold nanoparticles appear to be superior handles in optical trapping assays. We demonstrate that relatively large gold particles (R(b)=50 nm) indeed yield a sixfold enhancement in trapping efficiency and detection sensitivity as compared to similar-sized polystyrene particles. However, optical absorption by gold at the most common trapping wavelength (1064 nm) induces dramatic heating (266 degrees C/W). We determined this heating by comparing trap stiffness from three different methods in conjunction with detailed modeling. Due to this heating, gold nanoparticles are not useful for temperature-sensitive optical-trapping experiments, but may serve as local molecular heaters. Also, such particles, with their increased detection sensitivity, make excellent probes for certain zero-force biophysical assays.

Kinesin crouches to sprint but resists pushing

Recent optical trap experiments have applied resisting, assisting, and sideways loads to conventional kinesin moving on microtubules at fixed [ATP]. To gain insight into intermediate motions when the motor protein takes its 8.2-nm steps, the velocity and randomness data have been analyzed by using discrete-state stochastic models with a three-dimensional "energy landscape." The bead size and tether angle play a crucial role. The analysis implies that on binding ATP the motor "crouches," the point of attachment of the tether at the necklinker junction moving downward toward the microtubule by 0.5-0.7 nm, while inching forward by only 0.1-0.2 nm, before completing the step from a transition state by a unitary "sprint" of approximately 7.8 nm. These inferences accord with high-resolution observations that exclude a previously predicted substep of 1.8-2.1 nm. Assisting and leftward loads are opposed in that the perpendicular component of the tension in the tether is enhanced by approximately 2 pN, which reduces the velocity, but sideways lurching is not supported.

Study on the Nano-CMM Probe based on Laser Trapping Technology using an Optical Fiber : Fundamental Analysis of the Optical Fiber Trapping(Nano/micro measurement and intelligent instrument)

A novel three-dimensional probing technique for micro parts with high aspect ratios is proposed. In this technique, a particle trapped optically at the optical fiber tip is used as a probe for position detection. Numerical analysis about the optical force and detection signal were demonstrated by using finite difference time domain method (FDTD) and Maxwell stress tensor. And also fundamental optical fiber trapping experiments were demonstrated in the water. For the first, a probe sphere was levitated by illumination from the laser, and laser light emitted from the optical fiber successfully trapped the probe sphere three-dimensionally.

Measuring 01-nm motion in 1 ms in an optical microscope with differential back-focal-plane detection

Back-focal-plane detection of micrometer-sized beads offers subnanometer resolution for single-molecule, optical trapping experiments. However, laser beam-pointing instability and mechanical drift of the microscope limit the resolution of optical-trapping experiments. By combining two infrared lasers with improved differential beam-pointing stability (< or = 0.05 microrad), we simultaneously measure and subtract the motion of the microscope stage, leading to a resolution of <0.1 nm in 1 ms and stability of 0.5 nm over 60 s. Repeated steps of 0.4 nm at 1 Hz are resolved with a signal-to-noise ratio of 25.

Single atoms in optical traps

We present a brief overview of optical trapping experiments of individual neutral atoms. Then we describe in more details an experiment using a very small optical dipole trap, that is designed to store and manipulate individual atoms. Due to the very small dipole trap volume, a collisional blockade mechanism locks the average number of trapped atoms on the value 0.5 over a large range of loading rates. We study this regime experimentally, and we describe methods to measure the oscillation frequencies and the temperature of a single atom in the trap with a high accuracy.

Hyperfine quenching of the metastableP0,23states in divalent atoms

Hyperfine quenching rates of the lowest-energy metastable $^3P_0$ and $^3P_2$ states of Mg, Ca, Sr, and Yb atoms are computed. The calculations are carried out using ab initio relativistic many-body methods. The computed lifetimes may be useful for designing novel ultra-precise optical clocks and trapping experiments with the $3P_2$ fermionic isotopes. The resulting natural widths of the $^3P_0 -> ^1S_0$ clock transition are 0.44 mHz for $^{25}$Mg, 2.2 mHz for $^{43}$Ca, 7.6 mHz for $^{87}$Sr, 43.5 mHz for $^{171}$Yb, and 38.5 mHz for $^{173}$Yb. Compared to the bosonic isotopes, the lifetime of the $3P_2$ states in fermionic isotopes is noticeably shortened by the hyperfine quenching but still remains long enough for trapping experiments.

Mechanics of semiflexible chains formed by poly(ethylene glycol)-linked paramagnetic particles.

Magnetorheological particles, permanently linked into chains, provide a magnetically actuated means to manipulate microscopic fluid flow. Paramagnetic colloidal particles form reversible chains by acquiring dipole moments in the presence of an external magnetic field. By chemically connecting paramagnetic colloidal particles, flexible magnetoresponsive chains can be created. We link the paramagnetic microspheres using streptavidin-biotin binding. Streptavidin coated microspheres are placed in a flow cell and a magnetic field is applied, causing the particles to form chains. Then a solution of polymeric linkers of bis-biotin-poly(ethylene glycol) molecules is added in the presence of the field. These linked chains remain responsive to a magnetic field; however, in the absence of an external magnetic field these chains bend and flex due to thermal motion. The chain flexibility is determined by the length of the spacer molecule between particles and is quantified by the flexural rigidity or bending stiffness. To understand the mechanical properties of the chains, we use a variety of optical trapping experiments to measure the flexural rigidity. Increasing the length of the poly(ethylene glycol) chain in the linker increases the flexibility of the chains.

6] Building and using optical traps to study properties of molecular motors

Publisher Summary This chapter describes the building and using of optical traps to study the properties of molecular motors. Optical trapping experiments very directly measure the velocity, force, step size, and processive run length of molecular motors. The velocity, stall force, step size, and processive run length of molecular motors have all been determined using in vitro motility assays, both at the multiple- and the single-molecule levels. Optical trapping experiments in particular are used to gain information on stall forces, step sizes, and kinetics of a variety of molecular motors, such as kinesins, myosins, and processive DNA enzymes. Optical trapping assays are now performed on a variety of different systems using experimental techniques that may apply well to new, uncharacterized molecular motors and other biological macromolecules as well. These developments in both the technology and the assays involved in optical trapping have made the technique more accessible, increasing the likelihood that the optical trap can become a standard microscope used in laboratories that study movement and force in biological systems.

Configurational entropy and mechanical properties of cross-linked polymer chains: implications for protein and RNA folding.

We discuss the statistical mechanical properties of a single polymer chain that forms cross links among its monomers. Models of this type have served as prototypes in theories of RNA and protein folding. The chain is allowed to form pseudoknots and its monomers can each participate in multiple cross links. We demonstrate that the conformational free energy of such a chain can be estimated by using an algorithm that scales as a power of the number of cross links N(N1-N3, depending on the problem). Straightforward exact evaluation of the chain partition function via multidimensional integration scales exponentially with N and often is computationally prohibitive. Our approach can also be used to compute the "entropic force" generated by a cross-linked chain when it is stretched at its ends. Such forces can be directly measured by atomic force microscopy or by laser optical trap experiments performed on single RNA, DNA, and protein molecules.

Structural changes of pulled vesicles: A Brownian dynamics simulation

We studied the structural changes of bilayer vesicles induced by mechanical forces using a Brownian dynamics simulation. Two nanoparticles, which interact repulsively with amphiphilic molecules, are put inside a vesicle. The position of one nanoparticle is fixed, and the other is moved by a constant force as in optical-trapping experiments. First, the pulled vesicle stretches into a pear or tube shape. Then the inner monolayer in the tube-shaped region is deformed, and a cylindrical structure is formed between two vesicles. After stretching the cylindrical region, fission occurs near the moved vesicle. Soon after this the cylindrical region shrinks. The trapping force approximately 100 pN is needed to induce the formation of the cylindrical structure and fission.

Myosin VI is a processive motor with a large step size.

Myosin VI is a molecular motor involved in intracellular vesicle and organelle transport. To carry out its cellular functions myosin VI moves toward the pointed end of actin, backward in relation to all other characterized myosins. Myosin V, a motor that moves toward the barbed end of actin, is processive, undergoing multiple catalytic cycles and mechanical advances before it releases from actin. Here we show that myosin VI is also processive by using single molecule motility and optical trapping experiments. Remarkably, myosin VI takes much larger steps than expected, based on a simple lever-arm mechanism, for a myosin with only one light chain in the lever-arm domain. Unlike other characterized myosins, myosin VI stepping is highly irregular with a broad distribution of step sizes.

Noise-activated escape from a sloshing potential well.

We treat the noise-activated escape from a one-dimensional potential well of an overdamped particle, to which a periodic force of fixed frequency is applied. Near the well top, the relevant length scales and the boundary layer structure are determined. We show how behavior near the well top generalizes the behavior determined by Kramers, in the case without forcing. Our analysis includes the case when the forcing does not die away in the weak-noise limit. We discuss the relevance of scaling regimes, defined by the relative strengths of the forcing and the noise, to recent optical trap experiments.

Motion of RNA Polymerase along DNA: A Stochastic Model

RNA polymerase is a key transcription enzyme that moves along a DNA double helix to polymerize an RNA transcript. Recent progress in micromechanical experiments permits quantitative studies of forces and motion generated by the enzyme. We present in this paper a chemical kinetics description of RNA polymerase motion. The model is based on a classical chemical kinetics description of polymerization reactions driven by a free energy gain that depends on forces applied externally at the catalytic site. The RNA polymerase controlled activation barrier of the reaction is assumed to be strongly dependent on inhibitory internal strains of the RNA polymerase molecule. The sequence sensitivity of RNA polymerase is described by a linear coupling between the height of the activation barrier and the local DNA sequence. Our model can simulate optical trap experiments and allows us to study the dynamics of chemically halted complexes that are important for footprinting studies. We find that the effective stall force is a sequence-dependent, statistical quantity, whose distribution depends on the observation time. The results are consistent with the experimental observations to date.