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Tetramethylrhodamine

Tetramethylrhodamine is a fluorescent dye commonly used in biological research.
It is a derivative of rhodamine, a family of red-fluorescent dyes with excitation and emission wavelengths suitable for a variety of applications.
Tetramethylrhodamine is often employed as a labeling reagent for proteins, nucleic acids, and other biomolecules, allowing visualization and tracking in cellular and molecular studies.
Its bright fluorescence and photostability make it a valuable tool for flow cytometry, microscopy, and high-throughput screening.
Researchers can optimize the use of tetramethylrhodamine through AI-driven protocol comparisons on PubCompare.ai, locating the most reproducible and accurate procedures from literature, preprints, and patents to identify the optimal products and workflows.

Most cited protocols related to «Tetramethylrhodamine»

Wild-type Swiss-Webster mice (Taconic Farms, Inc.) were used for embryonic BBB functionality assays and expression profiles. Homozygous Tie2-GFP transgenic mice (Jackson laboratory, strain 003658) were used for BBB transcriptional profiling. Mfsd2a null mice21 (link) (MMRRC strain 032467-UCD) were maintained on C57Bl/6;129SVE mixed background and used for testing the involvement of MSFD2A in barrier-genesis. All animals were treated according to institutional and NIH guidelines approved by IACUC at Harvard Medical School.Deeply anaesthetized pregnant mice were used. Minimal volume of 10-kDa Dextran-Tetramethylrhodamine, Lysine Fixable (D3312 Invitrogen) was injected into the embryonic liver, while keeping the embryo connected to the maternal blood circulation through the umbilical cord. After three minutes of tracer circulation, embryonic heads were fixed by immersion in 4% paraformaldehyde (PFA) overnight at 4°C, cryopreserved in 30% sucrose and frozen in TissueTek OCT (Sakura). 12 µm sections were then collected and post fixed in 4% PFA at room temperature (RT) for 15 min, washed in PBS and co-stained with either α-PECAM antibody or with Isolectin B4 to visualize blood vessels (see Method section for details). P90 HRP injection and E17.5 cortex capillaries TEM imaging was done as previously described2 (link).
Publication 2014
Animals Biological Assay Blood Vessel Capillaries Cortex, Cerebral dextran tetramethylrhodamine Embryo Freezing Head Homozygote Immunoglobulins Institutional Animal Care and Use Committees Isolectins Liver Lysine Mice, Laboratory Mice, Transgenic Mouse, Swiss paraform Strains Submersion Sucrose Transcription, Genetic Umbilical Cord
CD45.2 C57BL/6 (B6) and CD45.1 B6 mice were from the National Cancer Institute or a colony maintained at the University of California, San Francisco. Mice lacking Sphk2 and carrying LoxP-flanked Sphk1 were on a B6/129 mixed background (Pappu et al., 2007 (link)). Lyve-1 Cre knockin mice on a B6/129 mixed background were generated as described in Fig. S1. Lyve-1 Cre+ Sphk1f/− or f/f Sphk2−/− mice were generated by intercrossing. Control mice were usually littermates and were always from the same intercross and carried at least one wild-type Sphk allele. Rosa26-YFP reporter mice (Srinivas et al., 2001 (link)) were provided by N. Killeen (University of California, San Francisco, San Francisco, CA). To generate BM chimeras, recipient CD45.2+ mice were lethally irradiated with 1,300 rads in two doses separated by 3 h and injected with 5 × 106 wild-type BM cells prepared from a CD45.1+ donor. In some experiments, ∼2 × 107 cells/ml were labeled with 3.3 µM CFSE (Invitrogen) or 10 µM 5-(and-6)-(((4-chloromethyl)benzoyl)amino)tetramethylrhodamine (CMTMR; Invitrogen) in RPMI 1640 containing 2% FCS for 20 min at 37°C, and were then washed by spinning through a layer of FCS. Labeled cells were resuspended at ∼2 × 107 cells/ml, and were treated with 10 ng/ml OB or PTX at 37°C for 10 min, washed twice in warm RPMI 1640 with 2% FCS and 10 mM Hepes, and transferred to recipient mice. Lymph collection was performed as previously described (Matloubian et al., 2004 (link)). In brief, under a stereomicroscope, lymph was drawn from the cysterna chyli using a fine borosilicate glass microcapillary pipette (Sutter Instrument Co.). Cell numbers determined by flow cytometry were divided by the volume of collected lymph to determine the concentration. Protocols were approved by the Institutional Animal Care and Use Committee of the University of California, San Francisco.
Publication 2010
(((4-chloromethyl)benzoyl)amino)-tetramethylrhodamine 5-(6)-carboxyfluorescein diacetate succinimidyl ester Alleles Cells Chimera Flow Cytometry HEPES Institutional Animal Care and Use Committees Lymph Mice, 129 Strain Mus RRAD protein, human sphingosine kinase 2, human tetramethylrhodamine Tissue Donors

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Publication 2015
Actins Biological Assay Bos taurus Buffers Cardiac Arrest Cell Motility Assays Cells Heart Homo sapiens Oxygen Phalloidine Protein Isoforms Proteins Regeneration tetramethylrhodamine Utrophin
LTR stainings were performed by incubating dissected L3 stage fat bodies in 100 nM LTR (Invitrogen) for 5 min. For immunofluorescent labeling, bisected larvae were fixed overnight in 3.7% paraformaldehyde at 4°C and blocked in PBS with 0.1% Triton X-100, 0.05% sodium deoxycholate, and 3% goat serum for 3 h followed by overnight incubations with primary and secondary antibodies in blocking buffer at 4°C (Juhász et al., 2008 (link); Pircs et al., 2012 (link)). We used chicken anti-GFP (1:1,500; Invitrogen), rabbit anti-Atg5 (1:100; Sigma-Aldrich), rabbit anti-Atg8a (1:500; provided by K. Kohler, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland; Barth et al., 2011 (link)), rabbit anti-p62 (1:2,000; Pircs et al., 2012 (link)), rabbit anti–active caspase 3 (1:300; Cell Signaling Technology), rat anti-Atg8a (1:300), and rat anti-Syx17 (1:300; this study) primary and Alexa Fluor 488 anti–chicken, Alexa Fluor 488 anti–rabbit, Alexa Fluor 568 anti–rat, and Alexa Fluor 647 anti–rabbit (all 1:1,500; Invitrogen) secondary antibodies. For TUNEL stainings, adult heads and half-thoraces were fixed in 3.7% paraformaldehyde overnight at 4°C and embedded into paraffin following standard protocols. Sections were processed using In Situ Cell Death Detection Kit, tetramethylrhodamine red (Roche) with SYTOX green DNA stain (Juhász et al., 2007 (link)). Images were obtained on a microscope (Axio Imager.M2; Carl Zeiss) equipped with a grid confocal unit (ApoTome.2; Carl Zeiss) at room temperature, using Plan-Neofluar 20×, 0.5 NA (air), 40×, 0.75 NA (air), and 100×, 1.3 NA (oil) objectives, a camera (AxioCam MRm; Carl Zeiss), and AxioVision software (Carl Zeiss). Microscope settings were identical for experiments of the same kind. Primary images were processed in AxioVision and Photoshop (Adobe) to produce final figures. Note that Alexa Fluor 568 or 647 channels are pseudocolored magenta.
Publication 2013
Adult alexa 568 alexa fluor 488 Alexa Fluor 647 Antibodies Antibodies, Blocking Buffers Caspase 3 Cell Death Chest Chickens Deoxycholic Acid, Monosodium Salt Fat Body Fluorescent Antibody Technique Goat Head In Situ Nick-End Labeling Larva Microscopy Paraffin Embedding paraform Rabbits Rosaniline Dyes Serum Staining Stains SYTOX Green tetramethylrhodamine Triton X-100
Histological examination of the ischemic brain was performed by NeuN and Fluoro Jade B as described previously by our lab (Q. G. Zhang et al., 2008 (link)). Briefly, after perfusion with 0.9% saline followed by 4% paraformaldehyde (PFA) in 0.1 M phosphate buffer (PB), the brains were post-fixed, cryoprotected with 30% sucrose until they sank and frozen sectioned (20 μm) in the coronal plane of the dorsal hippocampus (∼2.5-4.5 mm posterior from bregma). Every fifth section was collected and utilized for staining. Staining for NeuN and Fluoro Jade B was performed using a mouse anti-NeuN monoclonal antibody (1:500, Chemicon, MA, USA) and Fluoro Jade B (AG310, Chemicon) as described in detail previously by our laboratory (Q. G. Zhang et al., 2008 (link)). Images were captured on an LSM510 Meta confocal laser microscope (Carl Zeiss, Thornwood, NY) as described previously by our laboratory (C. Wakade et al., 2008 (link)). Cells that positively stained with NeuN and negatively stained with Fluoro Jade B were identified as “surviving neurons”; in contrast, double-stained yellow-colored cells represent CA1 neurons undergoing degeneration.
TUNEL staining was performed on the free-floating coronal sections using the In Situ Cell Death Detection Kit (Roche, Penzberg, Germany) following the manufacturer's instruction. Briefly, after washing with 0.1 % PBS-Triton-X100, the slides were permeabilized with 10 μg/ml proteinase K in 10 mM Tris/HCl (pH 7.4) for 15 min, and incubated with TUNEL reaction mixture including enzyme solution (TdT) and Tetramethylrhodamine (TMR)-labeled TUNEL-positive nucleotides in a humidified chamber for 1 h at 37 °C. Slides for negative control were incubated with the label solution without terminal transferase for TUNEL. Samples were analyzed with a LSM510 Meta confocal microscope. For quantitative analyses, the number of surviving neurons, and TUNEL-positive cells per 250 μm length of medial CA1 pyramidal cell layer was counted bilaterally in 4-5 sections per animal to provide a single value for each animal. A Mean ± SE was calculated from the data in each group (n = 6-8 animals) and statistical analysis performed as described below.
Publication 2009
Animals Antibodies, Anti-Idiotypic Brain Buffers CA1 Pyramidal Cell Area Cell Death Cells Endopeptidase K Enzymes Fluoro-Jade B In Situ Nick-End Labeling Laser Microscopy Microscopy, Confocal Monoclonal Antibodies Mus Neurons Normal Saline Nucleotides paraform Perfusion Phosphates Seahorses Sucrose tetramethylrhodamine Transferase Triton X-100 Tromethamine

Most recents protocols related to «Tetramethylrhodamine»

Cells were seeded in tissue-culture treated 24-well plates and allowed to grow until they reached 80% confluency. Mitochondrial membrane potential was estimated by Tetramethylrhodamine, Ethyl Ester, Perchlorate (TMRE) (T669, Invitrogen), by following the manufacturer’s indications. TMRE is a fluorogenic cationic dye which is selectively targeted to active mitochondria. Cells were washed twice with warm DPBS, calcium, magnesium (14040133, Invitrogen) and incubated with 500 μL of 0.5 μM TMRE probe diluted in DPBS, calcium, magnesium for 30 min at 37°C protected from the light. An unstained well was used as blank. Cells were washed with DPBS, calcium, magnesium twice and maintained in 300 μL DPBS, calcium, magnesium. TMRE fluorescence (λex = 548 nm, λem = 574 nm) was measured in a SpectraMax M2/M2e microplate reader (Molecular Devices). TMRE probe fluorescence was normalized with the total protein content of each well, which was determined by the Micro BCA Protein Assay Kit.
Publication 2024
A mitochondrial membrane potential assay kit (BioVision) was used according to the manufacturer’s instructions. Total cells were incubated with the fluorescent tetramethylrhodamine, ethyl (TMRE, 200 nM) dye for 20 min at 37 °C and 5% CO2. For the negative control, FCCP (carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazon, 20 μM) was added into one well and incubated at 37 °C for 10 min prior to TMRE addition. Following incubation, the stained cells were harvested and gently washed with the assay buffer. Fluorescence signal was measured at 549/575 nm of excitation/emission wavelengths using a Synergy H1 multi-mode microplate reader (BioTek). Two technical and biological replicates were performed for each sample.
Publication 2024

Example 122

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Tetramethylrhodamine formamidine 177. 5-Amino(tetramethyl)rhodamine 176 (0.100 g, 0.254 mmol), (chloromethylene)dimethylimminium chloride (0.155 g, 1.27 mmol), and DIEA (0.22 mL, 1.26 mmol) were stirred in 4 mL of DMF for 16 h. The reaction mixture was evaporated and the crude product was purified on a silica gel column (1.5×25 cm bed, patched in MeCN/H2O/AcOH (8:2:2.5)), eluant: MeCN/H2O/AcOH (8:2:2.5) to give amidine 177 (0.050 g, 48%) as a red solid.

Patent 2024
Amidines Anabolism Chlorides formamidine N,N-diisopropylethylamine Silica Gel tetramethylrhodamine
To measure mitochondrial superoxide and the mitochondrial membrane potential state, cells were labelled with 5 μM MitoSOX Red mitochondrial superoxide indicator reagent (ThermoFisher) or with 100 nM TMRM (ThermoFisher) and were incubated for 30 min at 37 ºC. Cells then were washed with PBS prior to cell surface staining as described above and analyzed by for flow cytometry.
Publication 2024
TMRM (#T668, Thermo Fisher Scientific) intensity (excitation/emission, 548/574 nm) was measured according to the manufacturer’s instructions Briefly, cells were added with staining solution at a final concentration of 100 nM and incubated for 30 min at 37 °C. After washing with PBS, the fluorescence was measured using SpectraMax i3. Results were normalized to the number of cells.
Publication 2024

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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
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MitoSOX Red is a fluorogenic dye designed to measure superoxide in the mitochondria of live cells. It is readily oxidized by superoxide but not by other reactive oxygen species. The oxidized product is highly fluorescent, allowing for the detection and quantification of mitochondrial superoxide.
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MitraTracker Green is a fluorescent dye used to label and monitor mitochondria in live cells. It passively diffuses across the cell membrane and accumulates in active mitochondria. The dye exhibits enhanced fluorescence upon binding to the mitochondrial membrane potential.
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Phalloidin-tetramethylrhodamine B isothiocyanate is a fluorescent dye that binds specifically to F-actin, a component of the cytoskeleton in eukaryotic cells. It is used in microscopy and flow cytometry applications to visualize and quantify actin filaments.
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Hoechst 33342 is a fluorescent dye that binds to DNA. It is commonly used in various applications, such as cell staining and flow cytometry, to identify and analyze cell populations.
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Triton X-100 is a non-ionic surfactant commonly used in various laboratory applications. It functions as a detergent and solubilizing agent, facilitating the solubilization and extraction of proteins and other biomolecules from biological samples.
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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MitoSOX is a fluorogenic dye that can be used to detect superoxide (O2-) in the mitochondria of live cells. It is a highly selective indicator of superoxide in the mitochondria.
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MitoTracker Green FM is a fluorescent dye that specifically labels mitochondria in live cells. It passively diffuses across the plasma membrane and accumulates in active mitochondria. The dye exhibits bright green fluorescence upon binding to mitochondrial lipids.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.

More about "Tetramethylrhodamine"

Tetramethylrhodamine (TRITC) is a versatile fluorescent dye widely used in biological research.
It is a member of the rhodamine family, a group of red-emitting fluorophores with excitation and emission wavelengths suitable for various applications.
TRITC is commonly employed as a labeling reagent for proteins, nucleic acids, and other biomolecules, enabling their visualization and tracking in cellular and molecular studies.
Its bright fluorescence and photostability make TRITC a valuable tool for techniques such as flow cytometry, microscopy, and high-throughput screening.
Researchers can optimize the use of TRITC through AI-driven protocol comparisons on PubCompare.ai, a platform that helps identify the most reproducible and accurate procedures from literature, preprints, and patents.
When working with TRITC, researchers may also utilize other fluorescent dyes like DAPI (for nuclear staining), MitoSOX Red (for detecting mitochondrial superoxide), MitoTracker Green (for labeling mitochondria), and Phalloidin-TRITC (for actin filament staining).
Hoechst 33342 is another common nuclear stain that can be used in conjunction with TRITC.
The efficiency of TRITC labeling can be affected by factors such as the concentration of Triton X-100 (a detergent used for permeabilization) and the presence of serum proteins like Bovine Serum Albumin (BSA).
Careful optimization of these parameters, as well as the TRITC concentration itself, is crucial for obtaining reliable and consistent results.
By leveraging the insights and data-driven workflows available on PubCompare.ai, researchers can identify the optimal TRITC products and protocols, leading to more reproducible and accurate experiments in their studies.