The momentum transfer to a scatterer from fluorescence photons was detected using an optical system that permits one to simultaneously measure the radiation force exerted on and fluorescence emission from the scatterer. The core of this technique is a partially metal covered dielectric bead optically trapped in a liquid with dye molecules. Fluorescence emission from the volume that includes the bead is measured simultaneously with the Brownian motion of the bead. The perturbed motion of the bead is a result of photon momentum transfer from the fluorescence of the dye to the trapped scatterer. The bead position fluctuations indicate the presence of the fluorescence and its bleaching nature. The results demonstrate the capability of the photonic force microscopy technique to be a complement to spectroscopy in the study of optical processes.
Friday, November 13, 2009
Experimental analysis of recoil effects induced by fluorescence photons
Alexander Zhdanov, Satish Rao, Andrey Fedyanin, and Dmitri Petrov
The momentum transfer to a scatterer from fluorescence photons was detected using an optical system that permits one to simultaneously measure the radiation force exerted on and fluorescence emission from the scatterer. The core of this technique is a partially metal covered dielectric bead optically trapped in a liquid with dye molecules. Fluorescence emission from the volume that includes the bead is measured simultaneously with the Brownian motion of the bead. The perturbed motion of the bead is a result of photon momentum transfer from the fluorescence of the dye to the trapped scatterer. The bead position fluctuations indicate the presence of the fluorescence and its bleaching nature. The results demonstrate the capability of the photonic force microscopy technique to be a complement to spectroscopy in the study of optical processes.
The momentum transfer to a scatterer from fluorescence photons was detected using an optical system that permits one to simultaneously measure the radiation force exerted on and fluorescence emission from the scatterer. The core of this technique is a partially metal covered dielectric bead optically trapped in a liquid with dye molecules. Fluorescence emission from the volume that includes the bead is measured simultaneously with the Brownian motion of the bead. The perturbed motion of the bead is a result of photon momentum transfer from the fluorescence of the dye to the trapped scatterer. The bead position fluctuations indicate the presence of the fluorescence and its bleaching nature. The results demonstrate the capability of the photonic force microscopy technique to be a complement to spectroscopy in the study of optical processes.
Physical methods and molecular biology
I. N. Serdyuk
The review is devoted to describing the current state of physical and chemical methods used for studying the structural and functional bases of vital processes. Special attention is focused on the physical methods that have opened a new page in the research on the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic tweezers. New physical methods, such as 2D infrared spectroscopy, fluorescence correlation spectroscopy, and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the last 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its view of the system in space and time. All physical methods are complementary. It is complementarity that is the fundamental idea justifying the existence in practice of all physical methods the description of which was the aim of the review.
The review is devoted to describing the current state of physical and chemical methods used for studying the structural and functional bases of vital processes. Special attention is focused on the physical methods that have opened a new page in the research on the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic tweezers. New physical methods, such as 2D infrared spectroscopy, fluorescence correlation spectroscopy, and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the last 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its view of the system in space and time. All physical methods are complementary. It is complementarity that is the fundamental idea justifying the existence in practice of all physical methods the description of which was the aim of the review.
Thursday, November 12, 2009
Translocation of RecA-Coated Double-Stranded DNA through Solid-State Nanopores
R. M. M. Smeets, S. W. Kowalczyk, A. R. Hall, N. H. Dekker and C. Dekker
We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10^−4−10^−1 s) and conductance blockade values (3−14 nS). Large blockades (11.4 ± 0.7 nS) are identified as being caused by translocations of RecA−dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (less than 150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.
We report translocation of double-stranded DNA (dsDNA) molecules that are coated with RecA protein through solid-state nanopores. Translocation measurements show current-blockade events with a wide variety in time duration (10^−4−10^−1 s) and conductance blockade values (3−14 nS). Large blockades (11.4 ± 0.7 nS) are identified as being caused by translocations of RecA−dsDNA filaments. We confirm these results through a variety of methods, including changing molecular length and using an optical tweezer system to deliver bead-functionalized molecules to the nanopore. We further distinguish two different regimes of translocation: a low-voltage regime (less than 150 mV) in which the event rate increases exponentially with voltage, and a high-voltage regime in which it remains constant. Our results open possibilities for a variety of future experiments with (partly) protein-coated DNA molecules, which is interesting for both fundamental science and genomic screening applications.
Irregular spin angular momentum transfer from light to small birefringent particles
M. Rothmayer, D. Tierney, E. Frins, W. Dultz, and H. Schmitzer
The transfer of spin angular momentum from photons to small particles is a key experiment of quantum physics. The particles rotate clockwise or counterclockwise depending on the polarization of the light beam which holds them in an optical trap. We show that even perfectly disk shaped particles will in general not rotate with a constant angular speed. The particles will periodically accelerate and decelerate their rotational motion due to a varying spin angular momentum transfer from the light. Using the Poincaré sphere we derive the equation of motion of a birefringent plate and verify the results by measuring the time dependent rotation of small crystals of Hg(I) iodide and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) in the trap of polarized optical tweezers. For small ellipticities of the polarized light in the tweezers the plate stops in a fixed orientation relative to the axes of the light ellipse. We discuss the origin of this halt and propose an application of small birefringent plates as self-adjusting optical retarders in micro-optics.
The transfer of spin angular momentum from photons to small particles is a key experiment of quantum physics. The particles rotate clockwise or counterclockwise depending on the polarization of the light beam which holds them in an optical trap. We show that even perfectly disk shaped particles will in general not rotate with a constant angular speed. The particles will periodically accelerate and decelerate their rotational motion due to a varying spin angular momentum transfer from the light. Using the Poincaré sphere we derive the equation of motion of a birefringent plate and verify the results by measuring the time dependent rotation of small crystals of Hg(I) iodide and 3,4,9,10-perylene-tetracarboxylic-dianhydride (PTCDA) in the trap of polarized optical tweezers. For small ellipticities of the polarized light in the tweezers the plate stops in a fixed orientation relative to the axes of the light ellipse. We discuss the origin of this halt and propose an application of small birefringent plates as self-adjusting optical retarders in micro-optics.
Nanomechanics of biomolecules: focus on DNA
Y. Eugene Pak, Dae Shick Kim, Mohana Marimuthu and Sanghyo Kim
Nano-mechanical measurements and manipulations at the single-cell and single-molecular levels using the atomic force microscope (AFM) and optical tweezers are presenting fascinating opportunities to the researchers in bioscience and biotechnology. Single molecule biophysics technologies, due to their capability to detect transient states of molecules and biomolecular complexes, are the methods of choice for studies in DNA structure and dynamics, DNA-DNA and DNA-protein interactions, and viral DNA packaging. The aim of this review is to describe the recent developments of scientific tools and the knowledge gained in single molecule DNA mechanics such as DNA elasticity, electrostatics, condensation and interactions of DNA with surrounding fluids during its hydrodynamic flow.
Nano-mechanical measurements and manipulations at the single-cell and single-molecular levels using the atomic force microscope (AFM) and optical tweezers are presenting fascinating opportunities to the researchers in bioscience and biotechnology. Single molecule biophysics technologies, due to their capability to detect transient states of molecules and biomolecular complexes, are the methods of choice for studies in DNA structure and dynamics, DNA-DNA and DNA-protein interactions, and viral DNA packaging. The aim of this review is to describe the recent developments of scientific tools and the knowledge gained in single molecule DNA mechanics such as DNA elasticity, electrostatics, condensation and interactions of DNA with surrounding fluids during its hydrodynamic flow.
Elimination of a zero-order beam induced by a pixelated spatial light modulator for holographic projection
Hao Zhang, Jinghui Xie, Juan Liu, and Yongtian Wang
A technique is proposed theoretically and verified experimentally to eliminate a zero-order beam caused by a pixelated phase-only spatial light modulator (SLM) for holographic projection. The formulas for determination of the optical field in the Fourier plane are deduced, and the influence of the pixelated structure of a SLM on the intensity of the zero-order beam is numerically investigated. Two currently existing techniques are studied and a new one is presented. These three techniques are used separately to eliminate the zero-order interruption, and the optical performances of the reconstructed patterns are compared. The new technique results in higher reconstruction quality and diffraction efficiency. A short animated movie is illuminated for holographic projection display. The experimental results show that the zero-order beam can be efficiently eliminated by the new technique. It is believed that this technique can be used in various optical systems that are based on pixelated phase-only SLMs, such as holographic optical tweezers and optical testing systems.
A technique is proposed theoretically and verified experimentally to eliminate a zero-order beam caused by a pixelated phase-only spatial light modulator (SLM) for holographic projection. The formulas for determination of the optical field in the Fourier plane are deduced, and the influence of the pixelated structure of a SLM on the intensity of the zero-order beam is numerically investigated. Two currently existing techniques are studied and a new one is presented. These three techniques are used separately to eliminate the zero-order interruption, and the optical performances of the reconstructed patterns are compared. The new technique results in higher reconstruction quality and diffraction efficiency. A short animated movie is illuminated for holographic projection display. The experimental results show that the zero-order beam can be efficiently eliminated by the new technique. It is believed that this technique can be used in various optical systems that are based on pixelated phase-only SLMs, such as holographic optical tweezers and optical testing systems.
Monitoring of Swelling and Degrading Behavior of Alginate Beads using Optical Tweezers
Lan Jin, You-Chan Hong, Jin-Woo Pyo, Hanwook Song, Ji Yoon Kang, Sang Woo Lee, Dae Sung Yoon, Beop-Min Kim & Kwangsoo No
Calcium alginate beads are widely used in drug delivery studies due to their high biocompatibility and the simple gelatinization process. It is well known that the alginate bead size changes in solutions with time, increasing initially and decreasing at a later stage. Therefore, it is essential to monitor or predict the size change of the beads since it affects the drug delivery efficiency significantly. We used the optical tweezers, a non-contact method, to investigate the temporal changes of the alginate beads in solutions instead of using the traditional drying and weighing technique. Responses to alginate concentration or external stimuli such as pH were also studied. The power spectrum method was utilized to estimate the trapping forces on the beads, which is related to the particle size changes. The results of our experiment indicate that the optical tweezers technique can continuously monitor the swelling and degrading of an alginate bead in an aqueous medium over hours which poses a high potential for drug encapsulation and release efficiency studies in the future.
Calcium alginate beads are widely used in drug delivery studies due to their high biocompatibility and the simple gelatinization process. It is well known that the alginate bead size changes in solutions with time, increasing initially and decreasing at a later stage. Therefore, it is essential to monitor or predict the size change of the beads since it affects the drug delivery efficiency significantly. We used the optical tweezers, a non-contact method, to investigate the temporal changes of the alginate beads in solutions instead of using the traditional drying and weighing technique. Responses to alginate concentration or external stimuli such as pH were also studied. The power spectrum method was utilized to estimate the trapping forces on the beads, which is related to the particle size changes. The results of our experiment indicate that the optical tweezers technique can continuously monitor the swelling and degrading of an alginate bead in an aqueous medium over hours which poses a high potential for drug encapsulation and release efficiency studies in the future.
DNA based molecular motors
Jens Michaelis, Adam Muschielok, Joanna Andrecka, Wolfgang Kügel and Jeffrey R. Moffitt
Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.
Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.
Tuesday, November 10, 2009
Thermo-optical resonance locking of an optically trapped salt-water microdroplet
Marc Guillon, Rachael E H Miles, Jonathan P Reid and David McGloin
We demonstrate that it is possible to lock the radius of an optically trapped salt-water microdroplet to then=1 whispering gallery resonances (WGRs) at the trapping laser wavelength. The optical properties of the droplet are determined using stimulated Raman scattering. The droplet is in thermodynamic equilibrium with the surrounding vapour and the proposed locking mechanism consists of a balance between bulk heating and WGR heating. Raman measurements allow the size parameter (nka) of the droplet to be determined with a precision of ~10−5 and the resonance linewidth to be estimated.
We demonstrate that it is possible to lock the radius of an optically trapped salt-water microdroplet to then=1 whispering gallery resonances (WGRs) at the trapping laser wavelength. The optical properties of the droplet are determined using stimulated Raman scattering. The droplet is in thermodynamic equilibrium with the surrounding vapour and the proposed locking mechanism consists of a balance between bulk heating and WGR heating. Raman measurements allow the size parameter (nka) of the droplet to be determined with a precision of ~10−5 and the resonance linewidth to be estimated.
Monday, November 9, 2009
Optical position clamping with predictive control
Heikki Ojala, Anders Korsbäck, Anders E. Wallin, and Edward Hæggström
We increase the effective stiffness of optical tweezers by position clamping a polystyrene bead with a predictive feedback control algorithm. This algorithm mitigates the effect of feedback loop delay. Hence, higher gain than with proportional control can be employed, which results in higher effective trap stiffness, without trap instability. In experiments (initial trap stiffness 0.056 pN/nm with a 1.78 µm diameter polystyrene bead), predictive control increased the effective trap stiffness by 55% relative to proportional control. We also derive theoretical expressions for the power spectra of the bead position controlled by our algorithm.
We increase the effective stiffness of optical tweezers by position clamping a polystyrene bead with a predictive feedback control algorithm. This algorithm mitigates the effect of feedback loop delay. Hence, higher gain than with proportional control can be employed, which results in higher effective trap stiffness, without trap instability. In experiments (initial trap stiffness 0.056 pN/nm with a 1.78 µm diameter polystyrene bead), predictive control increased the effective trap stiffness by 55% relative to proportional control. We also derive theoretical expressions for the power spectra of the bead position controlled by our algorithm.
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