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https://www.readbyqxmd.com/read/28439980/nanophotonic-trapping-precise-manipulation-and-measurement-of-biomolecular-arrays
#1
REVIEW
James E Baker, Ryan P Badman, Michelle D Wang
Optical trapping is a powerful and widely used laboratory technique in the biological and materials sciences that enables rapid manipulation and measurement at the nanometer scale. However, expanding the analytical throughput of this technique beyond the serial capabilities of established single-trap microscope-based optical tweezers remains a current goal in the field. In recent years, advances in nanotechnology have been leveraged to create innovative optical trapping methods that increase the number of available optical traps and permit parallel manipulation and measurement of arrays of optically trapped targets...
April 24, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28423909/ripping-rna-by-force-using-gaussian-network-models
#2
Changbong Hyeon, D Thirumalai
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict, studies in the context of proteins have shown that topology is the major determinant of the unfolding landscapes. By building on this finding we study the responses of RNA molecules to force by adapting Gaussian network model (GNM) that represents RNAs using a bead-spring network with isotropic interactions...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28414807/interactions-between-the-breast-cancer-associated-muc1-mucins-and-c-type-lectin-characterized-by-optical-tweezers
#3
Soosan Hadjialirezaei, Gianfranco Picco, Richard Beatson, Joy Burchell, Bjørn Torger Stokke, Marit Sletmoen
Carbohydrate-protein interactions govern many crucial processes in biological systems including cell recognition events. We have used the sensitive force probe optical tweezers to quantify the interactions occurring between MGL lectins and MUC1 carrying the cancer-associated glycan antigens mucins Tn and STn. Unbinding forces of 7.6 pN and 7.1 pN were determined for the MUC1(Tn)-MGL and MUC1(STn)-MGL interactions, at a force loading rate of ~40 pN/s. The interaction strength increased with increasing force loading rate, to 27 and 37 pN at a force loading rate of ~ 310 pN/s...
2017: PloS One
https://www.readbyqxmd.com/read/28373648/optimizing-phase-to-enhance-optical-trap-stiffness
#4
Michael A Taylor
Phase optimization offers promising capabilities in optical tweezers, allowing huge increases in the applied forces, trap stiff-ness, or measurement sensitivity. One key obstacle to potential applications is the lack of an efficient algorithm to compute an optimized phase profile, with enhanced trapping experiments relying on slow programs that would take up to a week to converge. Here we introduce an algorithm that reduces the wait from days to minutes. We characterize the achievable in-crease in trap stiffness and its dependence on particle size, refractive index, and optical polarization...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28365483/structural-transitions-in-torsionally-constrained-dna-and-their-dependence-on-solution-electrostatics
#5
Jaspreet Singh, Prashant K Purohit
Experimental studies on single molecules of DNA have reported a rich variety of structural transitions, including coexistence of three phases, in a torsionally constrained molecule. A comprehensive knowledge of these structural transitions is useful for unraveling the in vivo and in vitro behavior of DNA. Our objective is to understand the structural transitions in a torsionally constrained DNA molecule when it is pulled using optical or magnetic tweezers. We use foundational concepts from the Zimm-Bragg helix-coil transition theory and merge them with ideas from the theory of fluctuating elastic rods to model the mechanics of DNA...
March 29, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28362777/optical-concatenation-of-a-large-number-of-beads-with-a-single-beam-optical-tweezer
#6
Remy Avila, Joaquín Ascencio-Rodríguez, Daniel Tapia-Merino, Oscar G Rodríguez-Herrera, Arturo González-Suárez
Optical tweezers consist of the spatial confinement of microscopic dielectric particles by the action of forces produced by the change in momentum of the photons of a highly focused laser beam that are deviated by the particle. In experiments that use a single laser beam, it is common to capture not only one but a few particles in the optical trap. However, to our knowledge, the formation of a long chain of beads optically confined with a single laser beam has never been reported. In this work, up to 73 silica spheres immersed in water are seen concatenated along the propagation direction of a 976-nm wavelength Gaussian laser of 300 mW of power...
April 1, 2017: Optics Letters
https://www.readbyqxmd.com/read/28345878/multispectral-optical-tweezers-for-biochemical-fingerprinting-of-cd9-positive-exosome-subpopulations
#7
Randy P Carney, Sidhartha Hazari, Macalistair Colquhoun, Di Tran, Billanna Hwang, Michael S Mulligan, James D Bryers, Eugenia Girda, Gary S Leiserowitz, Zachary James Smith, Kit S Lam
Extracellular vesicles (EVs), including exosomes, are circulating nanoscale particles heavily implicated in cell signaling, and can be isolated in vast numbers from human biofluids. Study of their molecular profiling and materials properties is currently underway for purposes of describing a variety of biological functions and diseases. However, the large, and as yet unquantified, variety of EV subpopulations differing in composition, size, and likely function, necessitates characterization schemes capable of measuring single vesicles...
March 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28345092/integrating-optical-tweezers-with-up-converting-luminescence-a-non-amplification-analytical-platform-for-quantitative-detection-of-microrna-21-sequences
#8
Cheng-Yu Li, Di Cao, Chong-Yang Song, Chun-Miao Xu, Xu-Yan Ma, Zhi-Ling Zhang, Dai-Wen Pang, Hong-Wu Tang
We report a single-microsphere based imaging assay method by integrating up-converting luminescence with optical tweezers for detecting microRNA-21 sequences. This method achieves a competitive detection limit of 12 fM with good selectivity and no dedicated signal amplification designs.
March 27, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28329910/nucleosome-mobility-and-the-regulation-of-gene-expression-insights-from-single-molecule-studies
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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