keyword
MENU ▼
Read by QxMD icon Read
search

optical tweezers

keyword
https://www.readbyqxmd.com/read/28329910/nucleosome-mobility-and-the-regulation-of-gene-expression-insights-from-single-molecule-studies
#1
REVIEW
Sergei Rudnizky, Omri Malik, Adaiah Bavly, Lilach Pnueli, Philippa Melamed, Ariel Kaplan
Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA, and function as a basic layer in the complex regulation of gene expression. Our understanding of the role of the nucleosome's spontaneous, thermally driven position changes in modulating expression is lacking. This is the result of the paucity of experimental data on these dynamics, at high-resolution, and for DNA sequences that belong to real, transcribed genes. We have developed an assay that uses partial, reversible unzipping of nucleosomes with optical tweezers to repeatedly probe a nucleosome's position over time...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28303166/single-molecule-studies-of-high-mobility-group-b-architectural-dna-bending-proteins
#2
REVIEW
Divakaran Murugesapillai, Micah J McCauley, L James Maher, Mark C Williams
Protein-DNA interactions can be characterized and quantified using single molecule methods such as optical tweezers, magnetic tweezers, atomic force microscopy, and fluorescence imaging. In this review, we discuss studies that characterize the binding of high-mobility group B (HMGB) architectural proteins to single DNA molecules. We show how these studies are able to extract quantitative information regarding equilibrium binding as well as non-equilibrium binding kinetics. HMGB proteins play critical but poorly understood roles in cellular function...
February 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28298004/driven-optical-matter-dynamics-of-electrodynamically-coupled-nanoparticles-in-an-optical-ring-vortex
#3
Patrick Figliozzi, Nishant Sule, Zijie Yan, Ying Bao, Stanislav Burov, Stephen K Gray, Stuart A Rice, Suriyanarayanan Vaikuntanathan, Norbert F Scherer
To date investigations of the dynamics of driven colloidal systems have focused on hydrodynamic interactions and often employ optical (laser) tweezers for manipulation. However, the optical fields that provide confinement and drive also result in electrodynamic interactions that are generally neglected. We address this issue with a detailed study of interparticle dynamics in an optical ring vortex trap using 150-nm diameter Ag nanoparticles. We term the resultant electrodynamically interacting nanoparticles a driven optical matter system...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297655/formation-of-large-hypericin-aggregates-in-giant-unilamellar-vesicles-experiments-and-modeling
#4
Jaroslava Joniova, Matúš Rebič, Alena Strejčková, Veronika Huntosova, Jana Staničová, Daniel Jancura, Pavol Miskovsky, Gregor Bánó
The incorporation of hypericin (Hyp) from aqueous solutions into giant unilamellar vesicle (GUV) membranes has been studied experimentally and by means of kinetic Monte Carlo modeling. The time evolution of Hyp fluorescence originating from Hyp monomers dissolved in the GUV membrane has been recorded by confocal microscopy and while trapping individual GUVs in optical tweezers. It was shown that after reaching a maximum, the fluorescence intensity gradually decreased toward longer times. Formation of oversized Hyp clusters has been observed on the GUV surface at prolonged time...
March 14, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28296044/biolens-behavior-of-rbcs-under-optically-induced-mechanical-stress
#5
Francesco Merola, Álvaro Barroso, Lisa Miccio, Pasquale Memmolo, Martina Mugnano, Pietro Ferraro, Cornelia Denz
In this work, the optical behavior of Red Blood Cells (RBCs) under an optically-induced mechanical stress was studied. Exploiting the new findings concerning the optical lens-like behavior of RBCs, the variations of the wavefront refracted by optically-deformed RBCs were further investigated. Experimental analysis have been performed through the combination of digital holography and numerical analysis based on Zernike polynomials, while the biological lens is deformed under the action of multiple dynamic optical tweezers...
March 13, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28295322/the-%C3%AE-%C3%AE-circular-scanning-with-large-range-and-low-noise
#6
J Liu, X You, Y Wang, K Gu, C Liu, J Tan
A circular-route scanning method called α-β circular scanning is proposed and realized using sinusoidal signals with a constant phase difference of π/2. Experiments show that the circular scanning range of α-β circular scanning is 57% greater than the rectangular scanning range of raster scanning within an effective optical field of view. Moreover, the scanning speed is improved by 7.8% over raster scanning because the whole sine signal is utilized in α-β circular scanning whereas the flyback area of the saw-tooth signal needs to be discarded in raster scanning...
March 15, 2017: Journal of Microscopy
https://www.readbyqxmd.com/read/28287952/single-molecule-observation-of-dna-compaction-by-meiotic-protein-sycp3
#7
Johanna L Syrjänen, Iddo Heller, Andrea Candelli, Owen R Davies, Erwin J G Peterman, Gijs J L Wuite, Luca Pellegrini
In a previous paper (Syrjänen et al., 2014), we reported the first structural characterisation of a synaptonemal complex (SC) protein, SYCP3, which led us to propose a model for its role in chromosome compaction during meiosis. As a component of the SC lateral element, SYCP3 has a critical role in defining the specific chromosome architecture required for correct meiotic progression. In the model, the reported compaction of chromosomal DNA caused by SYCP3 would result from its ability to bridge distant sites on a DNA molecule with the DNA-binding domains located at each end of its strut-like structure...
March 13, 2017: ELife
https://www.readbyqxmd.com/read/28271103/a-liquid-thermal-gradient-refractive-index-lens-and-using-it-to-trap-single-living-cell-in-flowing-environments
#8
H L Liu, Y Shi, L Liang, L Li, S S Guo, L Yin, Y Yang
A gradient refractive index (GRIN) lens has a great potential for on-chip imaging and detection systems because of its flat surface with reduced defects. This paper reports a liquid thermal GRIN lens prepared using heat conduction between only one liquid, and uses it as a tunable optical tweezer for single living cell trapping in a flowing environment. This liquid GRIN lens consists of a trapezoidal region in the upper layer which is used to establish a GRIN profile by the heat conduction between three streams of benzyl alcohol with different temperatures, and subsequently a rhombus region in the lower layer with compensation liquids to form a steady square-law parabolic refractive index profile only in transverse direction...
March 8, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28270994/optical-sorting-and-cultivation-of-denitrifying-anaerobic-methane-oxidation-archaea
#9
Xiaoqiong Qi, David M Carberry, Chen Cai, Shihu Hu, Zhiguo Yuan, Halin Rubinsztein Dunlop, Jianhua Guo
Denitrifying anaerobic methane oxidizing (DAMO) microorganisms play an important role in the global carbon and nitrogen cycles as they are able to mediate methane oxidation using nitrite/nitrate under anoxic conditions. However, the physiological properties of DAMO microorganisms remain poorly understood, partially since the organisms are difficult to isolate or cultivate in pure culture and partially because of their long cultivation time. In this study, DAMO cell sorting has been conducted by integrating optical tweezers within enclosed microfluidic chips...
February 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28263430/single-molecule-mechanochemical-characterization-of-e-coli-pol-iii-core-catalytic-activity
#10
M Nabuan Naufer, David A Murison, Ioulia Rouzina, Penny J Beuning, Mark C Williams
Pol III core is the three-subunit subassembly of the E. coli replicative DNA polymerase III holoenzyme. It contains the catalytic polymerase subunit α, the 3' → 5' proofreading exonuclease ε, and a subunit of unknown function, θ. We employ optical tweezers to characterize pol III core activity on a single DNA substrate. We observe polymerization at applied template forces F<25 pN and exonucleolysis at F>30 pN. Both polymerization and exonucleolysis occur as a series of short bursts separated by pauses...
March 6, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28260487/structure-properties-and-biological-relevance-of-the-dna-and-rna-g-quadruplexes-overview-50-years-after-their-discovery
#11
N G Dolinnaya, A M Ogloblina, M G Yakubovskaya
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding-unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA-RNA G4s are discussed...
December 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28256218/switching-between-exonucleolysis-and-replication-by-t7-dna-polymerase-ensures-high-fidelity
#12
Tjalle P Hoekstra, Martin Depken, Szu-Ning Lin, Jordi Cabanas-Danés, Peter Gross, Remus T Dame, Erwin J G Peterman, Gijs J L Wuite
DNA polymerase catalyzes the accurate transfer of genetic information from one generation to the next, and thus it is vitally important for replication to be faithful. DNA polymerase fulfills the strict requirements for fidelity by a combination of mechanisms: 1) high selectivity for correct nucleotide incorporation, 2) a slowing down of the replication rate after misincorporation, and 3) proofreading by excision of misincorporated bases. To elucidate the kinetic interplay between replication and proofreading, we used high-resolution optical tweezers to probe how DNA-duplex stability affects replication by bacteriophage T7 DNA polymerase...
February 28, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28251048/detecting-swelling-states-of-red-blood-cells-by-cell-fluid-coupling-spectroscopy
#13
Carla Zensen, Isis E Fernandez, Oliver Eickelberg, Jochen Feldmann, Theobald Lohmüller
Red blood cells are "shaken" with a holographic optical tweezer array. The flow generated around cells due to the periodic optical forcing is measured with an optically trapped "detector" particle located in the cell vicinity. A signal-processing model that describes the cell's physical properties as an analog filter illustrates how cells can be distinguished from each other.
February 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://www.readbyqxmd.com/read/28248503/direct-observation-of-folding-energy-landscape-of-rna-hairpin-at-mechanical-loading-rates
#14
Huizhong Xu, Benjamin Plaut, Xiran Zhu, Maverick Chen, Udit Mavinkurve, Anindita Maiti, Guangtao Song, Krishna Murari, Maumita Mandal
By applying a controlled mechanical load using optical tweezers, we measured the diffusive barrier crossing in a 49 nt long P5ab RNA hairpin. We find that in the free-energy landscape the barrier height (G(‡)) and transition distance (x(‡)) are dependent on the loading rate (r) along the pulling direction, x, as predicted by Bell. The barrier shifted toward the initial state, whereas ΔG(‡) reduced significantly from 50 to 5 kT, as r increased from 0 to 32 pN/s. However, the equilibrium work (ΔG) during strand separation, as estimated by Crook's fluctuation theorem, remained unchanged at different rates...
March 1, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28248397/aberration-compensation-for-optical-trapping-of-cells-within-living-mice
#15
Min-Cheng Zhong, Zi-Qiang Wang, Yin-Mei Li
Optical tweezers have been used to trap and manipulate microparticles within living animals. When the optical trap is constructed with an oil-immersion objective, it suffers from spherical aberration. There have been many investigations on the influence of spherical aberration when the particles are trapped in a water medium. However, the dependence of optical force on trapping depth is still ambiguous when the trapped particles are immersed in a high refractive index medium (such as biological tissue, refractive index solution) in experiments...
March 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28230355/thermophoretic-tweezers-for-low-power-and-versatile-manipulation-of-biological-cells
#16
Linhan Lin, Xiaolei Peng, Xiaoling Wei, Zhangming Mao, Chong Xie, Yuebing Zheng
Optical manipulation of biological cells and nanoparticles is significantly important in life sciences, early disease diagnosis, and nanomanufacturing. However, low-power and versatile all-optical manipulation has remained elusive. Herein, we have achieved light-directed versatile thermophoretic manipulation of biological cells at an optical power 100-1000 times lower than that of optical tweezers. By harnessing the permittivity gradient in the electric double layer of the charged surface of the cell membrane, we succeed at the low-power trapping of suspended biological cells within a light-controlled temperature gradient field...
February 24, 2017: ACS Nano
https://www.readbyqxmd.com/read/28230298/vitamin-e-nanoemulsion-activity-on-stored-red-blood-cells
#17
C A L Silva, C A Azevedo Filho, G Pereira, D C N Silva, M C A B Castro, A F Almeida, S C A Lucena, B S Santos, M L Barjas-Castro, A Fontes
BACKGROUND: Stored red blood cells (RBCs) undergo numerous changes that have been termed RBC storage lesion, which can be related to oxidative damage. Vitamin E is an important antioxidant, acting on cell lipids. Thus, this study aimed to investigate vitamin E activity on stored RBCs. METHODS: We prepared a vitamin E nanoemulsion that was added to RBC units and stored at 4 °C. Controls, without vitamin E, were kept under the same conditions. Reactive oxygen species (ROS) production was monitored for up to 35 days of storage...
February 23, 2017: Transfusion Medicine
https://www.readbyqxmd.com/read/28222010/optical-tweezers-studies-of-transcription-by-eukaryotic-rna-polymerases
#18
Ana Lisica, Stephan W Grill
Transcription is the first step in the expression of genetic information and it is carried out by large macromolecular enzymes called RNA polymerases. Transcription has been studied for many years and with a myriad of experimental techniques, ranging from bulk studies to high-resolution transcript sequencing. In this review, we emphasise the advantages of using single-molecule techniques, particularly optical tweezers, to study transcription dynamics. We give an overview of the latest results in the single-molecule transcription field, focusing on transcription by eukaryotic RNA polymerases...
March 1, 2017: Biomolecular Concepts
https://www.readbyqxmd.com/read/28220855/extending-calibration-free-force-measurements-to-optically-trapped-rod-shaped-samples
#19
Frederic Català, Ferran Marsà, Mario Montes-Usategui, Arnau Farré, Estela Martín-Badosa
Optical trapping has become an optimal choice for biological research at the microscale due to its non-invasive performance and accessibility for quantitative studies, especially on the forces involved in biological processes. However, reliable force measurements depend on the calibration of the optical traps, which is different for each experiment and hence requires high control of the local variables, especially of the trapped object geometry. Many biological samples have an elongated, rod-like shape, such as chromosomes, intracellular organelles (e...
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28214480/nonlinear-actin-deformations-lead-to-network-stiffening-yielding-and-nonuniform-stress-propagation
#20
Bekele Gurmessa, Shea Ricketts, Rae M Robertson-Anderson
We use optical tweezers microrheology and fluorescence microscopy to apply nonlinear microscale strains to entangled and cross-linked actin networks, and measure the resulting stress and actin filament deformations. We couple nonlinear stress response and relaxation to the velocities and displacements of individual fluorescent-labeled actin segments, at varying times throughout the strain and varying distances from the strain path, to determine the underlying molecular dynamics that give rise to the debated nonlinear response and stress propagation of cross-linked and entangled actin networks at the microscale...
February 15, 2017: Biophysical Journal
keyword
keyword
73424
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"