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Single molecule localization

Rui Yan, Seonah Moon, Samuel J Kenny, Ke Xu
As an elegant integration of the spatial and temporal dimensions of single-molecule fluorescence, single-molecule localization microscopy (SMLM) overcomes the diffraction-limited resolution barrier of optical microscopy by localizing single molecules that stochastically switch between fluorescent and dark states over time. While this type of super-resolution microscopy (SRM) technique readily achieves remarkable spatial resolutions of ∼10 nm, it typically provides no spectral information. Meanwhile, current scanning-based single-location approaches for mapping the positions and spectra of single molecules are limited by low throughput and are difficult to apply to densely labeled (bio)samples...
February 14, 2018: Accounts of Chemical Research
Amu Gubu, Long Li, Ning Yan, Xiaoyun Zheng, Seonghyun Lee, Mengke Feng, Qiang Li, Xiaoguang Lei, Kyubong Jo, Xinjing Tang
Bioorthogonal metabolic DNA labelling with fluorochromes is a powerful strategy to visualize DNA molecules and their functions. Herein, we report the development of a new DNA metabolic labelling strategy enabled by the catalyst-free bioorthogonal ligation using vinyl thioether modified thymidine and o-quinolinone quinone methide. With the newly designed vinyl thioether-modified thymidine (VTdT), we added labelling tags on cellular DNA, which could further be linked to fluorochromes in cells. Therefore, we successfully visualized the DNA localization within cells as well as single DNA molecules without other staining reagents...
February 14, 2018: Chemistry: a European Journal
Michael Hausmann, Emma Wagner, Jin-Ho Lee, Gerrit Schrock, Wladimir Schaufler, Matthias Krufczik, Franziska Papenfuß, Matthias Port, Felix Bestvater, Harry Scherthan
Ionizing radiation (IR)-induced damage confers functional and conformational changes to nuclear chromatin associated with DNA single and double strand breaks. This leads to the activation of complex DNA repair machineries that aim to preserve the integrity of the DNA molecule. Since hetero- and euchromatin are differentially accessible to DNA repair pathways, local chromatin re-arrangements and structural changes are among the consequences of an activated DNA damage response. Using super-resolution localization microscopy (SRLM), we investigated the X-ray-induced repositioning of γ-H2AX and histone H3K9me3 heterochromatin marks in the nuclei of HeLa cells...
February 14, 2018: Nanoscale
Masahito Yamagata, Joshua R Sanes
Sensitive and specific antibodies are essential for detecting molecules in cells and tissues. However, currently used polyclonal and monoclonal antibodies are often less specific than desired, difficult to produce, and available in limited quantities. A promising recent approach to circumvent these limitations is to employ chemically defined antigen-combining domains called "nanobodies," derived from single-chain camelid antibodies. Here, we used nanobodies to prepare sensitive unimolecular detection reagents by genetically fusing cDNAs encoding nanobodies to enzymatic or antigenic reporters...
February 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jean Cacheux, Marie Brut, Aurélien Bancaud, Pierre Cordelier, Thierry Leichlé
In this work, we demonstrate that the analysis of spatially resolved nanofluidic-embedded biosensors permits the fast and direct discrimination of SND (single-nucleotide difference) within oligonucleotide sequences in a single step interaction. We design a sensor with a linear dimension much larger than the channel depth in order to ensure that the reaction over the whole sensor is limited by the convection rate. Thus, the targets are fully collected, inducing a non-uniform spatial hybridization profile. We also use the nanoscale height of the channel, which enables us to minimize the amount of labeled molecules flowing over the sensor and hence to reduce the fluorescence background, to carry out real-time hybridization detection by fluorescence microscopy...
February 13, 2018: ACS Sensors
Lior Bezen, Shira Yochelis, Dilhara Jayarathna, Dinesh C Bhunia, Catalina Achim, Yossi Paltiel
Devices based on self-assembled hybrid colloidal quantum dots (CQDs) coupled with specific organic linker molecules, are a promising way to simply realize room-temperature, spectrally-tunable light detectors. Nevertheless, this type of devices usually has low quantum efficiency. Plasmonics has been shown as an efficient tool in guiding and confining light at nanoscale dimensions. As plasmonic modes exhibit highly confined fields, they locally increase light-matter interactions and consequently enhance the performance of CQD-based photodetectors...
February 9, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Meng-Jiao Zhu, Jian-Bin Pan, Zeng-Qiang Wu, Xiao-Yu Gao, Wei Zhao, Xing-Hua Xia, Jing-Juan Xu, Hong-Yuan Chen
Noble metal nanoparticles are promising catalysts in electrochemical reactions, while understanding the relationship between the structure and reactivity of the particles is important to achieve higher efficiency of electrocatalysis, and promote the development of single-molecule electrochemistry. Herein, we employ electrogenerated chemiluminescence (ECL) to image the catalytic oxidation of luminophore at single Au, Pt and Au-Pt Janus nanoparticles. Compared to monometal, the Janus particle structure exhibited enhanced ECL intensity and stability, indicating better catalytic efficiency...
February 8, 2018: Angewandte Chemie
Jayeeta Kolay, Sudipta Bera, Tatini Rakshit, Rupa Mukhopadhyay
Realization of useful nanometre length scale devices in which metalloproteins are junction-confined in a distinct molecular arrangement for generating practical electronic signals (for example, in bioelectronic switch configuration), is elusive till date. This is mostly due to difficulties in observing electronically appropriate signal (i.e., reproducible and controllable), when studied under junction-assembled condition. A useful 'ON' - 'OFF' behaviour, based on the negative differential resistance (NDR) peak characteristics in the current-voltage response curves, acquired using metal-insulator-metal (MIM) configuration, has been observed only in case of a few proteins, namely, azurin, cytochrome C and bacteriorhodopsin, so far...
February 7, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Constanze Lamprecht, Mathias Gehrmann, Josef Madl, Winfried Römer, Gabriele Multhoff, Andreas Ebner
Hsp70-1A-the major stress-inducible member of the HSP70 chaperone family-is being implicated in cancer diseases with the development of resistances to standard therapies. In normal cells, the protein is purely cytosolic, but in a growing number of tumor cells, a significant fraction can be identified on to the cell surface. The anchoring mechanism is still under debate, as Hsp70-1A lacks conventional signaling sequences for translocation from the cytosol to exoplasmic leaflet of the plasma membrane and common membrane binding domains...
February 5, 2018: Cell Stress & Chaperones
Christoph S Werner, Boris Sturman, Evgeniy Podivilov, Sushanth Kini Manjeshwar, Karsten Buse, Ingo Breunig
Optical microresonators attract strong interest because of exciting effects and applications ranging from sensing of single atoms and molecules to quantum and nonlinear optics. For all this, control and tuning of the discrete resonances are vital. In resonators made of anisotropic materials that are beneficial for nonlinear-optical applications, anticrossings of ordinarily (o) and extraordinarily (e) polarized modes occur regularly. This effect is badly understood and harmful for mode control and tuning. We show that the anticrossings are inherent in the o- and e-modes because of the vectorial properties of Maxwell's equations...
January 22, 2018: Optics Express
Suman Das, Adam Eisen, Yi-Hsuan Lin, Hue Sun Chan
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding walks on the simple cubic lattice are constructed to study how phase behaviors depend on the sequence of monomers along the chains. To address pertinent general principles, we focus primarily on two fully charged 50-monomer sequences with significantly different charge patterns...
February 3, 2018: Journal of Physical Chemistry. B
Fenni Zhang, Wenwen Jing, Ashley Hunt, Hui Yu, Yunze Yang, Shaopeng Wang, Hong-Yuan Chen, Nongjian Tao
Measuring molecular binding to membrane proteins is critical for understanding cellular functions, validating biomarkers and screening drugs. Despite the importance, developing such a capability has been a difficult challenge, especially for small molecule binding to membrane proteins in their native cellular environment. Here we show that the binding of both large and small molecules to membrane proteins can be quantified on single cells by trapping single cells with a microfluidic device, and detecting binding-induced cellular membrane deformation on nanometer-scale with label-free optical imaging...
February 3, 2018: ACS Nano
Jiandong Feng, Hendrik Deschout, Sabina Caneva, Stephan Hofmann, Ivor Lončarić, Predrag Lazic, Aleksandra Radenovic
Point defects significantly influence the optical and electrical properties of solid-state materials due to their interactions with charge carriers, which reduce the band-to-band optical transition energy. There has been a demand for developing direct optical imaging methods that would allow in-situ characterization of individual defects with nanometer resolution. Here, we demonstrate the localization and quantitative counting of individual optically active defects in monolayer hexagonal boron nitride using single molecule localization microscopy...
February 2, 2018: Nano Letters
John Owoicho Orgah, Miao Wang, Xiaohu Yang, Zhilong Wang, Dandan Wang, Qi Zhang, Guanwei Fan, Jihong Han, Gangjian Qin, Xiumei Gao, Yan Zhu
BACKGROUND/AIMS: High blood pressure is a major risk factor for chronic kidney disease. Currently, single-target anti-hypertensive drugs are not designed for high blood pressure-related organ damages. Danhong injection (DHI), made from the aqueous extracts of Radix Salviae miltiorrhizae and Flos Carthamus tinctorius, has various pharmacological effects, including BP lowering in SHR, mediated by the reduction of vascular remodeling and the up-regulation of Kallikrein-kinin system published recently by our team, yet if it renders renal protection remains unknown...
January 23, 2018: Kidney & Blood Pressure Research
Shuangshuang Zhang, Shuanhu Qi, Leonid I Klushin, Alexander M Skvortsov, Dadong Yan, Friederike Schmid
We use Brownian dynamics simulations and analytical theory to compare two prominent types of single molecule transitions. One is the adsorption transition of a loop (a chain with two ends bound to an attractive substrate) driven by an attraction parameter ε and the other is the loop-stretch transition in a chain with one end attached to a repulsive substrate, driven by an external end-force F applied to the free end. Specifically, we compare the behavior of the respective order parameters of the transitions, i...
January 28, 2018: Journal of Chemical Physics
Ryan D Brown, Steven A Corcelli, S Alex Kandel
Traditionally, the goal of self-assembly and supramolecular chemistry is to engineer an equilibrium structure with a desired geometry and functionality; this is achieved through careful choice of molecular monomers, growth conditions, and substrate. Supramolecular assemblies produced under nonequilibrium conditions, in contrast, can form metastable structures with conformations quite different from those accessible in equilibrium self-assembly. The study of nonequilibrium growth of clusters potentially impacts the study of nucleation in atmospheric aerosols, nucleation in organic crystallization, and mesoscale organization for systems ranging from biological molecules to molecular electronics...
January 30, 2018: Accounts of Chemical Research
Hazen P Babcock
This work explores the use of industrial grade CMOS cameras for single molecule localization microscopy (SMLM). We show that industrial grade CMOS cameras approach the performance of scientific grade CMOS cameras at a fraction of the cost. This makes it more economically feasible to construct high-performance imaging systems with multiple cameras that are capable of a diversity of applications. In particular we demonstrate the use of industrial CMOS cameras for biplane, multiplane and spectrally resolved SMLM...
January 29, 2018: Scientific Reports
Mario Raab, Ija Jusuk, Julia Molle, Egbert Buhr, Bernd Bodermann, Detlef Bergmann, Harald Bosse, Philip Tinnefeld
In recent years, DNA origami nanorulers for superresolution (SR) fluorescence microscopy have been developed from fundamental proof-of-principle experiments to commercially available test structures. The self-assembled nanostructures allow placing a defined number of fluorescent dye molecules in defined geometries in the nanometer range. Besides the unprecedented control over matter on the nanoscale, robust DNA origami nanorulers are reproducibly obtained in high yields. The distances between their fluorescent marks can be easily analysed yielding intermark distance histograms from many identical structures...
January 29, 2018: Scientific Reports
Pengfei Zhan, Te Wen, Zhen-Gang Wang, Yingbo He, Jia Shi, Ting Wang, Xinfeng Liu, Guowei Lu, Baoquan Ding
Metallic bowtie nanoarchitecture can produce dramatic electric field enhancement which is advantageous in single molecule analysis and optical information processing. In the present study, we successfully constructed plasmonic bowtie nanostructures using a DNA origami-based bottom-up assembly strategy, which enables precise control over the geometrical configuration of the bowtie with an approximate 5 nm gap. We accurately positioned a single Raman probe at the gap of the bowtie. Single molecule surface-enhanced Raman scattering (SM-SERS) of individual nanostructures, including ones containing an alkyne group, was observed...
January 27, 2018: Angewandte Chemie
Joseph Murphy Brisendine, Sivan Refaely-Abramson, Zhen-Fei Liu, Jing Cui, Fay Ng, Jeffrey B Neaton, Ronald L Koder, Latha Venkataraman
We measure the conductance of unmodified peptides at the single molecule level using the scanning tunneling microscope-based break-junction method, utilizing the N-terminal amine group and the C-terminal carboxyl group as gold metal-binding linkers. Our conductance measurements of oligoglycine and oligoalanine backbones do not rely on peptide side-chain linkers. We compare our results with alkanes terminated asymmetrically with an amine group on one end and a carboxyl group on the other to show that peptide bonds decrease the conductance of an otherwise saturated carbon chain...
January 27, 2018: Journal of Physical Chemistry Letters
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