Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes.

ABSTRACT: Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. Such activatable probes with near-infrared (NIR) emission would be ideal for in vivo imaging but have proven difficult to engineer. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. We used the probes for mammalian cell surface imaging and, in conjunction with a new class of cyclooctyne D-amino acids, for visualization of bacterial peptidoglycan without the need to wash away unreacted probe.

SUBMITTER: Shieh P

PROVIDER: S-EPMC3992625 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes.

Shieh Peyton P Siegrist M Sloan MS Cullen Andrew J AJ Bertozzi Carolyn R CR

Proceedings of the National Academy of Sciences of the United States of America 20140331 15

Fluorescent probes designed for activation by bioorthogonal chemistry have enabled the visualization of biomolecules in living systems. Such activatable probes with near-infrared (NIR) emission would be ideal for in vivo imaging but have proven difficult to engineer. We present the development of NIR fluorogenic azide probes based on the Si-rhodamine scaffold that undergo a fluorescence enhancement of up to 48-fold upon reaction with terminal or strained alkynes. We used the probes for mammalian ...[more]

PMID: 24706769

Similar Datasets

Norcyanine-Carbamates Are Versatile Near-Infrared Fluorogenic Probes.

Project description:Fluorogenic probes in the near-infrared (NIR) region have the potential to provide stimuli-dependent information in living organisms. Here, we describe a new class of fluorogenic probes based on the heptamethine cyanine scaffold, the most broadly used NIR chromophore. These compounds result from modification of heptamethine norcyanines with stimuli-responsive carbamate linkers. The resulting cyanine carbamates (CyBams) exhibit exceptional turn-ON ratios (∼170×) due to dual requirements for NIR emission: carbamate cleavage through 1,6-elimination and chromophore protonation. Illustrating their utility in complex in vivo settings, a γ-glutamate substituted CyBam was applied to imaging γ-glutamyl transpeptidase (GGT) activity in a metastatic model of ovarian cancer. Overall, CyBams have significant potential to extend the reach of fluorogenic strategies to intact tissue and live animal imaging applications.

| S-EPMC9310664 | biostudies-literature

Rapid differentiation between bacterial infections and cancer using a near-infrared fluorogenic probe.

Project description:The reliable differentiation between bacterial infections and other pathologies is crucial for both diagnostics and therapeutic approaches. To accommodate such needs, we herein report the development of an activatable near-infrared fluorescent probe 1 that could be applied in the ultrafast, ultrasensitive and specific detection of nitroreductase (NTR) activity in bacterial pathogens both in vitro and in vivo. Upon reaction with NTR, the nitro-group of the para-nitro phenyl sulfonic moiety present in probe 1 was reduced to an amino-group, resulting in a near-infrared fluorescence turn-on of the latent cyanine 7 fluorophore. Probe 1 was capable of rapid and real-time quantitative detection of 0-150 ng mL-1 NTR with a limit of detection as low as 0.67 ng mL-1 in vitro. In addition, probe 1 exhibited an outstanding performance of ultrafast measurements and suitable selectivity toward NTR to accurately sense intracellular basal NTR in ESKAPE bacterial pathogens. Most remarkably, probe 1 was capable of noninvasively identifying bacterial infection sites without showing any significantly increased signal of tumour sites in the same animal within 30 min.

| S-EPMC8157330 | biostudies-literature

CalFluors: A Universal Motif for Fluorogenic Azide Probes across the Visible Spectrum.

Project description:Fluorescent bioorthogonal smart probes across the visible spectrum will enable sensitive visualization of metabolically labeled molecules in biological systems. Here we present a unified design, based on the principle of photoinduced electron transfer, to access a panel of highly fluorogenic azide probes that are activated by conversion to the corresponding triazoles via click chemistry. Termed the CalFluors, these probes possess emission maxima that range from green to far red wavelengths, and enable sensitive biomolecule detection under no-wash conditions. We used the CalFluor probes to image various alkyne-labeled biomolecules (glycans, DNA, RNA, and proteins) in cells, developing zebrafish, and mouse brain tissue slices.

| S-EPMC4487548 | biostudies-literature

A Near-Infrared Fluorogenic Pyrrole-Imidazole Polyamide Probe for Live-Cell Imaging of Telomeres.

Project description:Telomeres are closely associated with cellular senescence and cancer. Although some techniques have been developed to label telomeres in living cells for study of telomere dynamics, few biocompatible near-infrared probes based on synthetic molecules have been reported. In this study, we developed a near-infrared fluorogenic pyrrole-imidazole polyamide probe (SiR-TTet59B) to visualize telomeres by conjugating a silicon-rhodamine (SiR) fluorophore with a tandem tetramer pyrrole-imidazole polyamide targeting 24 bp in the telomeric double-stranded (ds) DNA. SiR-TTet59B was almost nonfluorescent in water but increased its fluorescence dramatically on binding to telomeric dsDNA. Using a peptide-based delivery reagent, we demonstrated the specific and effective visualization of telomeres in living U2OS cells. Moreover, SiR-TTet59B could be used to observe the dynamic movements of telomeres during interphase and mitosis. This simple imaging method using a synthetic near-infrared probe could be a powerful tool for studies of telomeres and for diagnosis.

| S-EPMC7683039 | biostudies-literature

Pre-Assembly of Near-Infrared Fluorescent Multivalent Molecular Probes for Biological Imaging.

Project description:A programmable pre-assembly method is described and shown to produce near-infrared fluorescent molecular probes with tunable multivalent binding properties. The modular assembly process threads one or two copies of a tetralactam macrocycle onto a fluorescent PEGylated squaraine scaffold containing a complementary number of docking stations. Appended to the macrocycle periphery are multiple copies of a ligand that is known to target a biomarker. The structure and high purity of each threaded complex was determined by independent spectrometric methods and also by gel electrophoresis. Especially helpful were diagnostic red-shift and energy transfer features in the absorption and fluorescence spectra. The threaded complexes were found to be effective multivalent molecular probes for fluorescence microscopy and in vivo fluorescence imaging of living subjects. Two multivalent probes were prepared and tested for targeting of bone in mice. A pre-assembled probe with 12 bone-targeting iminodiacetate ligands produced more bone accumulation than an analogous pre-assembled probe with six iminodiacetate ligands. Notably, there was no loss in probe fluorescence at the bone target site after 24 h in the living animal, indicating that the pre-assembled fluorescent probe maintained very high mechanical and chemical stability on the skeletal surface. The study shows how this versatile pre-assembly method can be used in a parallel combinatorial manner to produce libraries of near-infrared fluorescent multivalent molecular probes for different types of imaging and diagnostic applications, with incremental structural changes in the number of targeting groups, linker lengths, linker flexibility, and degree of PEGylation.

| S-EPMC4918808 | biostudies-literature

Oxygen-doped carbon nanotubes for near-infrared fluorescent labels and imaging probes.

Project description:Chemical modification of carbon nanotube surface can controllably modulate their optical properties. Here we report a simple and effective synthesis method of oxygen-doped single-walled carbon nanotubes (o-SWCNTs), in which a thin film of SWCNTs is just irradiated under the UV light for a few minutes in air. By using this method, the epoxide-type oxygen-adducts (ep-SWCNTs) were produced in addition to the ether-type oxygen-adducts (eth-SWCNTs). The Treated (6, 5) ep-SWCNTs show a red-shifted luminescence at ~1280 nm, which corresponds to the most transparent regions for bio-materials. Immunoassay, fluorescence vascular angiography and observation of the intestinal contractile activity of mice were demonstrated by using the produced o-SWCNTs as infrared fluorescent labels and imaging agents.

| S-EPMC5908862 | biostudies-literature

A near-infrared fluorogenic dimer enables background-free imaging of endogenous GPCRs in living mice.

Project description:Fluorescent probes are commonly used in studying G protein-coupled receptors in living cells; however their application to the whole animal receptor imaging is still challenging. To address this problem, we report the design and the synthesis of the first near-infrared emitting fluorogenic dimer with environment-sensitive folding. Due to the formation of non-fluorescent H-aggregates in an aqueous medium, the near-infrared fluorogenic dimer displays a strong turn-on response (up to 140-fold) in an apolar environment and exceptional brightness: 56% quantum yield and ≈444 000 M-1 cm-1 extinction coefficient. Grafted on a ligand of the oxytocin receptor, it allows the unprecedented background-free and target-specific imaging of the naturally expressed receptor in living mice.

| S-EPMC7504901 | biostudies-literature

Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes.

Project description:Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs.

| S-EPMC5578081 | biostudies-literature

Two new, near-infrared, fluorescent probes as potential tools for imaging bone repair.

Project description:A precise imaging technique to evaluate osteogenesis, osteodifferentiation, and osseointegration following peri-implant surgery is in high clinical demand. Herein, we report the generation of two new, near-infrared (NIR) fluorescent probes for use in the molecular imaging of bone repair. The first probe aims to monitor the in vitro differentiation of human mesenchymal stem cells (MSCs) into osteoblasts. A NIR fluorochrome was conjugated to a cyclic peptide that binds to integrin ?5?1, a factor that promotes osteogenesis in MSCs and therefore functioned as an osteoblast-specific marker. The second probe aims to monitor osteogenesis, and was generated by conjugating the drug pamidronate to a NIR fluorescent gold nanocluster. Pamidronate specifically binds to hydroxyapatite (HA), a mineral present in bone that is produced by osteoblasts, and therefore provides a functional marker for new bone formation. Our results show that both probes bind to their specific targets in vitro-differentiated osteoblasts, and not to undifferentiated MSCs, and emit NIR fluorescence for functional detection. This in vitro work demonstrates the ability of these probes to bind to active osteoblasts and their mineral deposits and highlight their potential utility as clinical tools for the imaging of the osseointegration process at the molecular level.

| S-EPMC7018698 | biostudies-literature

Near-infrared phosphorescent polymeric nanomicelles: efficient optical probes for tumor imaging and detection.

Project description:We report a formulation of near-infrared (near-IR) phosphorescent polymeric nanomicelles and their use for in vivo high-contrast optical imaging, targeting, and detection of tumors in small animals. Near-IR phosphorescent molecules of Pt(II)-tetraphenyltetranaphthoporphyrin (Pt(TPNP)) were found to maintain their near-IR phosphorescence properties when encapsulated into phospholipid nanomicelles. The prepared phosphorescent micelles are of approximately 100 nm size and are highly stable in aqueous suspensions. A large spectral separation between the Pt(TPNP) absorption, with a peak at approximately 700 nm, and its phosphorescence emission, with a peak at approximately 900 nm, allows a dramatic decrease in the level of background autofluorescence and scattered excitation light in the near-IR spectral range, where the signal from the phosphorescent probe is observed. In vivo animal imaging with subcutaneously xenografted tumor-bearing mice has resulted in high contrast optical images, indicating highly specific accumulation of the phosphorescent micelles into tumors. Using optical imaging with near-IR phosphorescent nanomicelles, detection of smaller, visually undetectable tumors has also been demonstrated.

| S-EPMC3681954 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data