scholarly journals Analytical Currents: STED microscopy illuminates vesicle fate | Imaging of the oxidant peroxynitrite in living cells | Solid immersion lenses made from PDMS | Molecular sorting in microfluidic devices | DNA sequencing on a chip | Single-molecule binding assay in femtoliter arrays | Simple derivatization of glycopeptides for MALDI | Direct electrical detection of DNA synthesis

2006 ◽  
Vol 78 (13) ◽  
pp. 4239-4242
Keyword(s):  
Dna Sequencing ◽  
Dna Synthesis ◽  
Single Molecule ◽  
Binding Assay ◽  
Microfluidic Devices ◽  
Living Cells ◽  
Electrical Detection ◽  
Sted Microscopy

scholarly journals Blinking fluorescent probes for tubulin nanoscopy in living and fixed cells

2021 ◽  
Author(s):  
Ruta Gerasimaite ◽  
Jonas Bucevicius ◽  
Kamila A. Kiszka ◽  
Georgij Kostiuk ◽  
Tanja Koenen ◽  
...  
Keyword(s):  
Small Molecule ◽  
Single Molecule ◽  
Fluorescent Probes ◽  
Living Cells ◽  
Stimulated Emission ◽  
Sted Microscopy ◽  
Linker Length ◽  
Localisation Microscopy ◽  
Red Dye ◽  
Small Molecule Probe

Here we report a small molecule probe for single molecule localisation microscopy (SMLM) of tubulin in living and fixed cells. We explored a series of constructs composed of taxanes and spontaneously blinking far-red dye hydroxymethyl silicon-rhodamine (HMSiR). We found that the linker length profoundly affects the probe permeability and off-targeting. The best performing probe, HMSiR-tubulin, is composed of cabazitaxel and 6'-regioisomer of HMSiR bridged by a C6 linker. Microtubule diameters of <50 nm can be routinely measured in SMLM experiments on living and fixed cells. HMSiR-tubulin also performs well in 3D stimulated emission depletion (STED) microscopy, allowing a complementary use of both nanoscopy methods for investigating microtubule functions in living cells.

scholarly journals Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array

2016 ◽  
Vol 113 (44) ◽  
pp. E6749-E6756 ◽  
Author(s):  
P. Benjamin Stranges ◽  
Mirkó Palla ◽  
Sergey Kalachikov ◽  
Jeff Nivala ◽  
Michael Dorwart ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Dna Synthesis ◽  
Lipid Bilayers ◽  
High Throughput ◽  
Single Molecule ◽  
Low Cost ◽  
Electrode Array ◽  
Oxide Semiconductor ◽  
Sequencing Platform ◽  
Sequencing By Synthesis

Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin–polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis. The designed nanopore construct successfully detected the capture of tagged nucleotides complementary to a DNA base on a provided template. We measured over 200 tagged-nucleotide signals for each of the four bases and developed a classification method to uniquely distinguish them from each other and background signals. The probability of falsely identifying a background event as a true capture event was less than 1.2%. In the presence of all four tagged nucleotides, we observed sequential additions in real time during polymerase-catalyzed DNA synthesis. Single-polymerase coupling to a nanopore, in combination with the Nanopore-SBS approach, can provide the foundation for a low-cost, single-molecule, electronic DNA-sequencing platform.

In-plane Graphene/h-BN/Graphene Heterostructures with Nanopore for Electrical Detection of DNA Nucleotides

2021 ◽  
Author(s):  
Ali Kiakojouri ◽  
Irmgard Frank ◽  
Ebrahim Nadimi
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Electrical Characteristics ◽  
Electrical Detection

The in-plane heterostructure of graphene and h-BN has unique physical and electrical characteristics, which can be exploited for single-molecule DNA sequencing. On this account, we propose a nanostructure based on...

Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

2019 ◽  
Author(s):  
Jiajun Wang ◽  
Meng-Yin Li ◽  
Jie Yang ◽  
Ya-Qian Wang ◽  
Xue-Yuan Wu ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Genetic Diseases ◽  
High Sensitivity ◽  
Dna Lesions ◽  
Lesion Detection ◽  
The Novel ◽  
Structural Variations ◽  
Dna Lesion ◽  
Base Lesion

DNA lesion such as metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i> could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C, <sup>O</sup>G, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

A Molecular Logic Gate Enables Super-Resolved Imaging of Intracellular Lipid Droplets

2019 ◽  
Author(s):  
Adam Eördögh ◽  
Carolina Paganini ◽  
Dorothea Pinotsi ◽  
Paolo Arosio ◽  
Pablo Rivera-Fuentes
Keyword(s):  
Single Molecule ◽  
Lipid Droplets ◽  
Neutral Lipids ◽  
Logic Gate ◽  
Living Cells ◽  
Three Dimensions ◽  
Single Molecule Imaging ◽  
Molecular Logic Gate ◽  
Molecular Logic ◽  
Cellular Compartments

<div>Photoactivatable dyes enable single-molecule imaging in biology. Despite progress in the development of new fluorophores and labeling strategies, many cellular compartments remain difficult to image beyond the limit of diffraction in living cells. For example, lipid droplets, which are organelles that contain mostly neutral lipids, have eluded single-molecule imaging. To visualize these challenging subcellular targets, it is necessary to develop new fluorescent molecular devices beyond simple on/off switches. Here, we report a fluorogenic molecular logic gate that can be used to image single molecules associated with lipid droplets with excellent specificity. This probe requires the subsequent action of light, a lipophilic environment and a competent nucleophile to produce a fluorescent product. The combination of these requirements results in a probe that can be used to image the boundary of lipid droplets in three dimensions with resolutions beyond the limit of diffraction. Moreover, this probe enables single-molecule tracking of lipids within and between droplets in living cells.</div>

scholarly journals A binding protein regulates myosin-7a dimerization and actin bundle assembly

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rong Liu ◽  
Neil Billington ◽  
Yi Yang ◽  
Charles Bond ◽  
Amy Hong ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Actin Filament ◽  
Single Molecule ◽  
Binding Protein ◽  
Living Cells ◽  
Actin Bundle ◽  
Actin Bundles ◽  
Cytoskeletal Remodeling ◽  
Actin Protrusions

AbstractMyosin-7a, despite being monomeric in isolation, plays roles in organizing actin-based cell protrusions such as filopodia, microvilli and stereocilia, as well as transporting cargoes within them. Here, we identify a binding protein for Drosophila myosin-7a termed M7BP, and describe how M7BP assembles myosin-7a into a motile complex that enables cargo translocation and actin cytoskeletal remodeling. M7BP binds to the autoinhibitory tail of myosin-7a, extending the molecule and activating its ATPase activity. Single-molecule reconstitution show that M7BP enables robust motility by complexing with myosin-7a as 2:2 translocation dimers in an actin-regulated manner. Meanwhile, M7BP tethers actin, enhancing complex’s processivity and driving actin-filament alignment during processive runs. Finally, we show that myosin-7a-M7BP complex assembles actin bundles and filopodia-like protrusions while migrating along them in living cells. Together, these findings provide insights into the mechanisms by which myosin-7a functions in actin protrusions.

scholarly journals Inhibition of DNA synthesis in living cells by microinjection of Gi2 antibodies.

1992 ◽  
Vol 267 (2) ◽  
pp. 691-694 ◽  
Author(s):  
V J LaMorte ◽  
P K Goldsmith ◽  
A M Spiegel ◽  
J L Meinkoth ◽  
J R Feramisco
Keyword(s):  
Dna Synthesis ◽  
Living Cells ◽  
Inhibition Of Dna Synthesis
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