Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer

Peter C. Anthony, Christian F. Perez, Cuauhtémoc García-García, and Steven M. Block

Riboswitches are motifs in the untranslated regions (UTRs) of RNA transcripts that sense metabolite levels and modulate the expression of the corresponding genes for metabolite import, export, synthesis, or degradation. All riboswitches contain an aptamer: an RNA structure that, upon binding ligand, folds to expose or sequester regulatory elements in the adjacent sequence through alternative nucleotide pairing. The coupling between ligand binding and aptamer folding is central to the regulatory mechanisms of thiamine pyrophosphate (TPP) riboswitches and has not been fully characterized. Here, we show that TPP aptamer folding can be decomposed into ligand-independent and -dependent steps that correspond to the formation of secondary and tertiary structures, respectively. We reconstructed the full energy landscape for folding of the wild-type (WT) aptamer and measured perturbations of this landscape arising from mutations or ligand binding. We show that TPP binding proceeds in two steps, from a weakly to a strongly bound state. Our data imply a hierarchical folding sequence, and provide a framework for understanding molecular mechanism throughout the TPP riboswitch family.

DOI

The integration of a micropipette in a closed microfluidic chip with optical tweezers for investigations of single cells: erratum

Ahmed Alrifaiy and Kerstin Ramser

In July 2011 a new concept of a closed microfluidic system equipped with a fixed micropipette, optical tweezers and a UV-Vis spectrometer was presented [Biomed. Opt. Express 2, 2299 (2011)]. Figure 1 showed falsely oriented mirrors. To clarify the design of the setup, this erratum presents a correct schematic.

DOI

Raman microspectroscopy detects epigenetic modifications in living Jurkat leukemic cells

Mathilde Poplineau, Aurélie Trussardi-Régnier, Teddy Happillon, Jean Dufer, Michel Manfait, Philippe Bernard,Olivier Piot & Frank Antonicelli

Classical biochemical and molecular methods for discerning cells with epigenetic modifications are often biologically perturbing or even destructive. We wondered whether the noninvasive laser tweezer Raman spectroscopy technique allowed the discrimination of single living human cells undergoing epigenetic modifications. Human Jurkat leukemic cells were treated with inhibitors of histone deacetylases (trichostatin A and MS-275). Epigenetic changes were monitored through histone electrophoresis, nuclear image cytometry and laser tweezer Raman spectroscopy. Treatment of Jurkat cells with histone deacetylase inhibitors increased histone acetylation and induced chromatin organization changes. Characteristic vibrations, issued from laser tweezer Raman spectroscopy analyses, mostly assigned to DNA and proteins allowed discerning histone deacetylase inhibitor-treated cells from control with high confidence. Statistical processing of laser tweezer Raman spectroscopy data led to the definition of specific biomolecular fingerprints of each cell group. This original study shows that laser tweezer Raman spectroscopy is a label-free rapid tool to identify living cells that underwent epigenetic changes.

DOI

Complex field-stabilised nematic defect structures in Laguerre–Gaussian optical tweezers

Tine Porenta, Miha Ravnik and Slobodan Zumer

Novel optical field-stabilised defect structures are presented in nematic liquid crystals as produced by Laguerre–Gaussian optical beams. Our modelling study is based on the phenomenological free energy approach. To mimic generic experiments, Laguerre–Gaussian optical beams of various helical indices are applied to a nematic cell. The symmetry of these field-stabilised nematic structures is directly determined by the beam indices. We show that the structures can also be tuned by the beam intensity and the strength of the nematic elastic constant. Finally, local intensity-induced control of the nematic order via absorption of the beam is demonstrated as a complementary mechanism for producing and tuning the nematic field-stabilised structures.

DOI

Radiation forces of a dielectric medium plate induced by a Gaussian beam

Donghua Li, Jixiong Pu, Xiqing Wang

Based on the angular spectrum method, we investigate the radiation forces on a finite-size dielectric medium plate induced by a Gaussian beam. The formulas for the radiation force along longitudinal and transverse direction are derived, and numerically calculation is performed. It is shown that for the finite-size dielectric medium plate, the radiation forces exerted by the Gaussian beam is dependent upon the angle and position of a single ray striking on the plate and the intensity of light. Our numerical results indicate that if we choose the appropriate parameters there will be enough transverse forces to overcome the gravity force, making the plate move upwards.

DOI

Optically Trapped Gold Nanoparticle Enables Listening at the Microscale

Alexander Ohlinger, Andras Deak, Andrey A. Lutich, and Jochen Feldmann

We explore a new application of optical tweezers for ultrasensitive detection of sound waves in liquid media. Position tracking of a single gold nanoparticle confined in a three-dimensional optical trap is used to readout acoustic vibrations at a sound power level down to -60  dB, causing a ∼90  μeV increase in kinetic energy of the nanoparticle. The unprecedented sensitivity of such a nanoear is achieved by processing the nanoparticle’s motion in the frequency domain. The concept developed here will enable us to access the interior of biological microorganisms and micromechanical machines not accessible by other microscopy types.

DOI

Application of plasmonic bowtie nanoantenna arrays for optical trapping, stacking, and sorting

Brian James Roxworthy, Kaspar D Ko, Anil Kumar, Kin Hung Fung, Edmond K.C. Chow, Gang Logan Liu, Nicholas Fang, and Kimani Christopher Toussaint

We present the use of Au bowtie nanoantenna arrays (BNAs) for highly efficient, multipurpose particle manipulation with unprecedented low input power and low-numerical aperture (NA) focusing. Optical trapping efficiencies measured are up to 20x the efficiencies of conventional high-NA optical traps and are among the highest reported to date. Empirically obtained plasmonic optical trapping "phase diagrams" are introduced to detail the trapping response of the BNAs as a function of input power, wavelength, polarization, particle diameter and BNA array spacing (number density). Using these diagrams, parameters are chosen, employing strictly the degrees-of-freedom of the input light, to engineer specific trapping tasks including: (1) dexterous, single-particle trapping and manipulation, (2) trapping and manipulation of 2 and 3-dimensional particle clusters, and (3) particle sorting. The use of low input power densities (power and NA) suggests that this bowtie nanoantenna trapping system will be particularly attractive for lab-on-a-chip technology or biological applications aimed at reducing specimen photodamage.

DOI

Particle separation in fluidic flow by optical fiber

Hongxiang Lei, Yao Zhang, and Baojun Li

We report a separation of two different size particles in fluidic flow by an optical fiber. With a light of 1.55 μm launched into the fiber, particles in stationary water were massively trapped and assembled around the fiber by a negative photophoretic force. By introducing a fluidic flow, the assembled particles were separated into two different downstream positions according to their sizes by the negative photophoretic force and the dragging force acted on the particles. The intensity distribution of light leaked from the fiber and the asymmetry factor of energy distribution have been analysed as crucial factors in this separation. Poly(methyl methacrylate) particles (5-/10-μm diameter), SiO2 particles (2.08-/5.65-μm diameter), and SiO2particles (2.08-μm diameter) mixed with yeast cells were used to demonstrate the effectiveness of the separation. The separation mechanism has also been numerical simulated and theoretical interpreted.

DOI

Directed assembly of optically bound matter

Michael D. Summers, Richard D. Dear, Jonathan M. Taylor, and Grant A.D. Ritchie

We present a study of optically bound matter formation in a counter-propagating evanescent field, exploiting total internal reflection on a prism surface. Small ensembles of silica microspheres are assembled in a controlled manner using optical tweezers. The structures and dynamics of the resulting optically bound chains are interpreted using a simulation implementing generalized Lorentz-Mie theory. In particular, we observe enhancement of the scattering force along the propagation direction of the optically bound colloidal chains leading to a microscopic analogue of a driven pendulum which, at least superficially, resembles Newton’s cradle.

DOI

Published Papers Statistics for 2011

Here is the long awaited results for the year of 2011 for published papers on optical tweezers, micromanipulation and trapping, in this blog (a total of 455 posts for 2011).

The top Journals (more than 2% hits) are:
Optics Express                             11%
Journal of Optics                            6%
Optics Letters                                5%
Nano Letters                                  4%
Lab on a Chip                                3%
Applied Physics Letters                  3%
Soft Matter                                    3%
Biophysical Journal                         2%
Physical Review Letters                  2%
Applied Optics                               2%
Nature Photonic                              2%
Proc. of the Nat. Acad. of Sci.         2%
Review of Scientific Instruments       2%

Below is also a tag cloud (from the words found in the title and abstracts for 2011):