scholarly journals Recent Advances in Organelle-Targeted Fluorescent Probes

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 217
Author(s):  
Na-Eun Choi ◽  
Ji-Yu Lee ◽  
Eun-Chae Park ◽  
Ju-Hee Lee ◽  
Jiyoun Lee
Keyword(s):  
Fluorescent Probes ◽  
Molecular Level ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Structural Features ◽  
Future Directions ◽  
Cellular Processes ◽  
Biochemical Pathways ◽  
Recent Advances ◽  
Super Resolution Microscopy

Recent advances in fluorescence imaging techniques and super-resolution microscopy have extended the applications of fluorescent probes in studying various cellular processes at the molecular level. Specifically, organelle-targeted probes have been commonly used to detect cellular metabolites and transient chemical messengers with high precision and have become invaluable tools to study biochemical pathways. Moreover, several recent studies reported various labeling strategies and novel chemical scaffolds to enhance target specificity and responsiveness. In this review, we will survey the most recent reports of organelle-targeted fluorescent probes and assess their general strategies and structural features on the basis of their target organelles. We will discuss the advantages of the currently used probes and the potential challenges in their application as well as future directions.

scholarly journals Recent Progress in Small Spirocyclic, Xanthene-Based Fluorescent Probes

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5964
Author(s):  
Sascha G. Keller ◽  
Mako Kamiya ◽  
Yasuteru Urano
Keyword(s):  
Small Molecules ◽  
Fluorescent Probes ◽  
Recent Progress ◽  
Super Resolution ◽  
Short Introduction ◽  
Computational Approaches ◽  
Recent Advances ◽  
Silicon Carbon ◽  
Super Resolution Microscopy ◽  
Made In

The use of fluorescent probes in a multitude of applications is still an expanding field. This review covers the recent progress made in small molecular, spirocyclic xanthene-based probes containing different heteroatoms (e.g., oxygen, silicon, carbon) in position 10′. After a short introduction, we will focus on applications like the interaction of probes with enzymes and targeted labeling of organelles and proteins, detection of small molecules, as well as their use in therapeutics or diagnostics and super-resolution microscopy. Furthermore, the last part will summarize recent advances in the synthesis and understanding of their structure–behavior relationship including novel computational approaches.

scholarly journals Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

2021 ◽  
Vol 22 (4) ◽  
pp. 1903
Author(s):  
Ivona Kubalová ◽  
Alžběta Němečková ◽  
Klaus Weisshart ◽  
Eva Hřibová ◽  
Veit Schubert
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Chromatin Condensation ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Wide Field ◽  
Structured Illumination Microscopy ◽  
Metaphase Chromosomes ◽  
Localization Microscopy ◽  
Super Resolution Microscopy

The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.

Super-resolution imaging of bacterial pathogens and visualization of their secreted effectors

2020 ◽  
Author(s):  
Moirangthem Kiran Singh ◽  
Linda J Kenney
Keyword(s):  
Virulence Factors ◽  
Protein Secretion ◽  
Fluorescent Probes ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Bacterial Pathogenesis ◽  
Secretion Systems ◽  
Complex Protein ◽  
Resolution Imaging ◽  
Protein Secretion Systems

ABSTRACT Recent advances in super-resolution imaging techniques, together with new fluorescent probes have enhanced our understanding of bacterial pathogenesis and their interplay within the host. In this review, we provide an overview of what these techniques have taught us about the bacterial lifestyle, the nucleoid organization, its complex protein secretion systems, as well as the secreted virulence factors.

Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy

2018 ◽  
Vol 141 (7) ◽  
pp. 2770-2781 ◽  
Author(s):  
Lu Wang ◽  
Michelle S. Frei ◽  
Aleksandar Salim ◽  
Kai Johnsson
Keyword(s):  
Small Molecule ◽  
Fluorescent Probes ◽  
Super Resolution ◽  
Live Cell ◽  
Super Resolution Microscopy

scholarly journals Super-Resolution Microscopy of Chromatin

Genes ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 493 ◽  
Author(s):  
Birk
Keyword(s):  
Gene Regulation ◽  
Data Analysis ◽  
Super Resolution ◽  
Fluorescence Labeling ◽  
Cellular Processes ◽  
Direct Assessment ◽  
Chromatin Interactions ◽  
Resolution Imaging ◽  
Super Resolution Microscopy ◽  
Insight Into

Since the advent of super-resolution microscopy, countless approaches and studies have been published contributing significantly to our understanding of cellular processes. With the aid of chromatin-specific fluorescence labeling techniques, we are gaining increasing insight into gene regulation and chromatin organization. Combined with super-resolution imaging and data analysis, these labeling techniques enable direct assessment not only of chromatin interactions but also of the function of specific chromatin conformational states.

scholarly journals Intracellular Delivery of Membrane Impermeable Photostable Fluorescent Probes into Living Cells for Super-Resolution Microscopy

2017 ◽  
Vol 112 (3) ◽  
pp. 21a
Author(s):  
Yuji Ishitsuka ◽  
Kai Wen Teng ◽  
Pin Ren ◽  
Yeoan Youn ◽  
Xiang Deng ◽  
...  
Keyword(s):  
Fluorescent Probes ◽  
Super Resolution ◽  
Intracellular Delivery ◽  
Living Cells ◽  
Super Resolution Microscopy

scholarly journals Ligand Geometry Controls Adhesion formation via Integrin Clustering

2018 ◽  
Author(s):  
Rishita Changede ◽  
Haogang Cai ◽  
Shalom Wind ◽  
Michael P. Sheetz
Keyword(s):  
Adhesion Formation ◽  
Focal Adhesions ◽  
Super Resolution ◽  
Total Width ◽  
Cellular Processes ◽  
Cell Matrix ◽  
Integrin Clustering ◽  
Super Resolution Microscopy ◽  
Fiber Mesh

AbstractIntegrin-mediated cell matrix adhesions are key to sensing the geometry and rigidity of the extracellular environment to regulate vital cellular processes. In vivo, the extracellular matrix (ECM) is composed of a fibrous mesh. To understand the geometry that supports adhesion formation on fibrous substrates, we patterned 10 nm gold-palladium single lines or pairs of lines (total width within 100 nm), mimicking thin single ECM fibers or a minimal mesh geometry, respectively and functionalized it with integrin binding ligand Arg-Gly-Asp (RGD). Single lines showed reduced focal adhesion kinase (FAK) recruitment and did not support cell spreading or formation of focal adhesions, despite the presence of a high density of integrin-binding ligands. Using super resolution microscopy, we observed transient integrin clusters on single lines, whereas stable 110 nm integrin clusters formed on pairs of lines similar to those on continuous substrates. This indicated that two-dimensional ligand geometry is required for adhesion formation on rigid substrates. A mechanism to form modular 100nm integrin clusters bridging the minimal fiber mesh would require unliganded integrins. We observed that integrin mutants unable to bind ligand co-clustered with ligand-bound integrins when present in an active extended conformation. Thus, these results indicate that functional integrin clusters are required to form focal adhesions and unliganded integrins can co-cluster to bridge between thin matrix fibers and can form stable integrin adhesions on dense fibrous networks.

scholarly journals Interphase Human Chromosome Exhibits Out of Equilibrium Glassy Dynamics

2017 ◽  
Author(s):  
Guang Shi ◽  
Lei Liu ◽  
Changbong Hyeon ◽  
D. Thirumalai
Keyword(s):  
Ostwald Ripening ◽  
Imaging Techniques ◽  
Mean Square Displacement ◽  
Super Resolution ◽  
Spatial Distance ◽  
Base Pairs ◽  
Glassy Dynamics ◽  
Distance Information ◽  
Contact Maps ◽  
Super Resolution Microscopy

AbstractThe structural organization of the condensed chromosomes is being revealed using chromosome conformation capture experiments and super-resolution imaging techniques. Fingerprints of their three-dimensional organization on length scale from about hundred kilo base pairs to millions of base pairs have emerged using advances in Hi-C and super-resolution microscopy. To determine the poorly understood dynamics of human interphase chromosomes, we created the Chromosome Copolymer Model (CCM) by representing the chromosomes as a self-avoiding polymer with two loci types corresponding to euchromatin and heterochromatin. Using advanced clustering algorithms we establish quantitatively that the simulated contact maps for chromosomes 5 and 10 and those inferred from Hi-C experiments are in agreement. Ward Linkage Matrix (WLM), constructed from spatial distance information, shows that the Topologically Associated Domains (TADs) and compartments predicted from simulations are in agreement with inferred WLM computed using data from super-resolution microscopy experiments. Glassy dynamics is manifested in the stretched exponential relaxation of the structure factor and caging in the mean square displacement of individual loci, ∆i(t) ∼ tα with 0 < α < 1. Remarkably, the distribution of α, is extremely broad suggestive of highly heterogeneous dynamics, which is also reflected in the large cell-to-cell variations in the contact maps. Chromosome organization is hierarchical involving the formation of chromosome droplets (CDs) on short genomic scale followed by coalescence of the CDs, reminiscent of Ostwald ripening. We propose that glassy landscapes for the condensed active chromosomes might provide a balance between genomic conformational stability and biological functions.

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