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IRDye800

IRDye800 is a near-infrared fluorescent dye commonly used in biomedical research and clinical applications.
It has a long excitation and emission wavelength range, allowing for deep tissue imaging and reduced autofluorescence.
PubCompare.ai's AI-driven protocol analysis tools help researchers optimize their IRDye800 experiments by identifying the most reproducible and accurate methods from literature, preprints, and patents.
This ensures superior results and improved IRDye800 research outcomes.
PubCompare.ai's advanced platform compares protocols side-by-side to locate the best approaches, saving time and enhanceing the quality of your IRDye800 studies.

Most cited protocols related to «IRDye800»

HeLa cells were purchased from the Human Science Research Resources Bank (Sennanshi, Japan). The Cos7 cells used were Cos7/E3, a subclone of Cos7 cells established by Y. Fukui (National Research Institute of Health, Taiwan, Republic of China). HeLa cells and Cos7 cells were maintained in DMEM (Sigma-Aldrich, St. Louis, MO) supplemented with 10% FBS. The cells were plated on 35-mm glass base dishes or 96-well glass base plates (Asahi Techno Glass, Tokyo, Japan), which were coated with collagen type I (Nitta Gelatin, Osaka, Japan). Plasmids encoding FRET biosensors were transfected into HeLa cells and Cos7 cells by 293fectin or Lipofectamine 2000, according to the manufacturer's instructions (Invitrogen, San Diego, CA), respectively. EGF was purchased from Sigma-Aldrich. dbcAMP, TPA, Calyculin A, Anisomycin, PD153035, and JNK inhibitor VIII were purchased from Calbiochem (La Jolla, CA). PD184352 was obtained from Toronto Research Chemicals (Ontario, Canada). BI-D1870 was purchased from Symansis (Shanghai, China). Rapamycin was obtained from LC Laboratories (Woburn, MA). PLX-4720 was purchased from Selleck Chemicals (Houston, TX). The expression vector of piggyBac transposase was provided by A. Bradley (Wellcome Trust Sanger Institute, Cambridge, UK; Yusa et al., 2009 (link)). Phos-tag was obtained from the Phos-tag Consortium (Hiroshima, Japan; www.phos-tag.com). Anti-green fluorescence protein (GFP) sera were prepared in our laboratory. LI-COR (Lincoln, NE) blocking buffer and the IRDye680- and IRDye800-conjugated anti–rabbit and anti–mouse immunoglobulin G secondary antibodies were obtained from LI-COR.
Publication 2011
1,3-bis(bis(pyridin-2-ylmethyl)amino)propan-2-ol Anisomycin Anti-Antibodies BI D1870 Biosensors Bucladesine Buffers calyculin A Cells Cloning Vectors Collagen Type I Fluorescence Resonance Energy Transfer Gelatins Green Fluorescent Proteins HeLa Cells Hyperostosis, Diffuse Idiopathic Skeletal Immunoglobulin G IRDye800 lipofectamine 2000 Manpower Mus PD 153035 PD 184352 Plasmids PLX 4720 Rabbits Serum Sirolimus Transposase
Commercially available NIR fluorophores included IRDye™ 800-CW (CW800; Li-Cor, Lincoln, NE), IRDye™ 800-RS (RS800; Li-Cor), and indocyanine green (ICG; Akorn, Decatur, IL). When only an NHS ester was available, the corresponding carboxylic acid (CA) was formed by incubation at high concentration in 50 mM borate buffer, pH 9.0 for 3 h followed by dilution into the desired buffer. All optical measurements were performed at 37°C in phosphate-buffered saline (PBS), pH 7.4 or 100% fetal bovine serum (FBS) buffered with 50 mM HEPES, pH 7.4. For fluorescence quantum yield (Φ) measurements, ICG in dimethyl sulfoxide (Φ = 13%) was used as a calibration standard under conditions of matched absorbance at 770 nm.[14 (link)-19 (link)] For in vitro optical property measurements, online fiberoptic HR2000 absorbance (200-1100 nm) and USB2000FL fluorescence (350-1000 nm) spectrometers (Ocean Optics, Dunedin, FL) were used. NIR excitation was provided by a 770 nm NIR laser diode light source (Electro Optical Components, Santa Rosa, CA) set to 8 mW and coupled through a 300-μm core diameter, NA 0.22 fiber (Fiberguide Industries, Stirling, NJ). In silico calculations of the partition coefficient (logD) and surface molecular charge and hydrophobicity were calculated using MarvinSketch 5.2.1 (ChemAxon, Budapest, Hungary).
Publication 2011
Borates Carboxylic Acids Esters Eye Fetal Bovine Serum Fibrosis Fluorescence HEPES Indocyanine Green IRDye800 Lasers, Semiconductor Phosphates Rosa Saline Solution Sulfoxide, Dimethyl Technique, Dilution Vision
Cell pellets were frozen in a dry ice/ethanol bath and lysed by bead disruption in NP-40 lysis buffer in either native or denaturing conditions as previously described (Gould et al., 1991 (link)), except with the addition of 0.1–0.5 mM diisopropyl fluorophosphate (Sigma-Aldrich). Proteins were immunoprecipitated by anti-HA (12CA5) or anti-FLAG (M2; Sigma-Aldrich) antibodies or a serum raised against GST-Cdc15 (amino acids 1–405; VU326; Cocalico Biologicals). Western blot analysis was performed as previously described (Wolfe et al., 2006 (link)) except that secondary antibodies were conjugated to Alexa Fluor 680 (Invitrogen) or IRDye800 (LI-COR Biosciences) and visualized using an Odyssey machine (LI-COR Biosciences).
For purification of Fic1-TAP, cells were lysed as described previously (Tasto et al., 2001 (link)), and protein was purified on tosylactivated Dynabeads (Invitrogen) coated with rabbit IgG (MP Biomedicals). Purified complexes were washed thoroughly and eluted with 0.5 M NH4OH and 0.5 mM EDTA or by TEV protease (Invitrogen) cleavage at 18°C for 1 h for use in immunoprecipitation experiments. For MS analysis, proteins were resuspended in 100 mM NH4HCO3 and 8 M urea, reduced and alkylated with Tris (2-carboxyethyl) phosphine and iodoacetamide, and digested with sequencing-grade trypsin (Promega) after decreasing to 2 M urea. MS was performed as previously described (McDonald et al., 2002 ) with the following modifications. Peptides were loaded onto columns with a pressure cell and were separated and analyzed by three-phase multidimensional protein identification technology on a linear trap quadrupole instrument (Thermo Electron). An autosampler (FAMOS) was used for 12 salt elution steps, each with 2 μl ammonium acetate. Each injection was followed by elution of peptides with a 0–40% acetonitrile gradient except the first and last injections, in which a 0–90% acetonitrile gradient was used. Eluted ions were analyzed by one full precursor MS scan (400–2,000 mass-to-charge ratio) and four tandem MS scans of the most abundant ions detected in the precursor MS scan under dynamic exclusion. The S. pombe database was searched using the SEQUEST algorithm, and results were processed using the CHIPS program (jointly developed by the Vanderbilt University Mass Spectrometry Research Center and University of Arizona). Filter settings for peptides were Xcorr ≥ 1.8 for singly charged, Xcorr ≥ 2.5 for doubly charged, and Xcorr ≥ 3.3 for triply charged.
Recombinant proteins were produced in chemically competent BL21 cells and purified on GST-Bind Resin (EMD), amylose beads (New England Biolabs, Inc.), or His-Bind resin (EMD) according to the manufacturers' protocols. For in vitro binding assays, recombinant proteins were incubated together for 1 h at 4°C. For lysate binding assays, cell lysates were incubated with bead-bound protein for 1 h at 4°C. In both cases, beads were washed thoroughly, and proteins were resolved by SDS-PAGE for Coomassie staining or Western blot analysis. Binding affinity experiments were performed as described previously (Disanza et al., 2004 (link)).
Publication 2009
acetonitrile Amino Acids ammonium acetate Amylose Antibodies Bath Biological Assay Biological Factors Buffers Cells Cytokinesis DNA Chips Dry Ice Edetic Acid Electrons Ethanol Freezing Immunoprecipitation Iodoacetamide Ions IRDye800 Isoflurophate Mass Spectrometry Nonidet P-40 Pellets, Drug Peptides phosphine Pressure Promega Proteins Rabbits Radionuclide Imaging Recombinant Proteins Resins, Plant Schizosaccharomyces pombe SDS-PAGE Serum Sodium Chloride Strains Tasto TEV protease Tromethamine Trypsin Urea Western Blot
Cell extracts were prepared by lysing cells on ice for 15 minutes by the addition of lysis buffer containing 20 mmol/L Tris.HCl, 138 mmol/L NaCl, 2.7 mmol/L KCl, pH 8.0, supplemented with 5% glycerol, 1 mmol/L MgCl2, 1 mmol/L CaCl2, 1 mmol/L sodium‐o‐vanadate, 20 μmol/L leupeptin, 18 μmol/L pepstatin, 1% NP‐40, 5 mmol/L EDTA, and 20 mmol/L NaF. Cell debris and nuclei were removed by centrifugation at 10 000×g for 10 minutes at 4°C. Protein concentration was determined with the Bio‐Rad DC Protein Assay kit, according to the manufacturer's instruction. Extracts (40 μg) were subjected to SDS‐PAGE and were electrophoretically transferred to an Immobilon‐P membrane (Millipore), and the resultant membrane was incubated overnight with the corresponding first antibody at 4°C, with gentle agitation after blocking with 5% skimmed milk. The protein was then decorated with corresponding anti‐mouse (Alexa Fluor 680–conjugated) or anti‐rabbit (IRDye 800–conjugated) secondary antibodies. Signals were visualized with Odyssey Infrared Imaging System (LI‐COR Biosciences). Quantification of the signals was performed in NIH Image 1.62 software.
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Publication 2012
Antibodies Biological Assay Buffers Cell Extracts Cell Nucleus Cells Centrifugation Edetic Acid Glycerin Immobilon P Immunoglobulins IRDye800 leupeptin Magnesium Chloride Milk, Cow's Mus Nonidet P-40 pepstatin Proteins Rabbits RRAD protein, human SDS-PAGE Sodium Chloride Sodium Vanadate Tissue, Membrane Tromethamine
The following samples were used to detect glycosylation of the indicated proteins in Fig. 1c: 293T whole cell lysate (Sp1), rat hypothalamus crude nuclear pellet (MeCP2), rat brain detergent-soluble fraction (synapsin IIa, Nup62), whole cell lysate from cultured embryonic neurons (CREB), cytosolic fraction from PUGNAc-treated cultured embryonic neurons (OGA), and p75-OGT purified from Sf9 cells. For Fig. 3a, the liver, hippocampus or cerebral cortex was harvested from adult Sprague Dawley rats, and crude nuclear pellets were processed. Animal protocols were approved by the Institutional Animal Care and Use Committee at Caltech, and the procedures were performed in accordance with the Public Health Service Policy on Humane Care and Use of Laboratory Animals. Cell lysates were prepared as described in the Supplementary Methods. Each sample and its corresponding negative control (lacking ketogalactose probe 1 incorporation) was subjected to chemoenzymatic labeling with PEG mass tags, resolved on 4–12% Bis-Tris NuPAGE gels (Invitrogen), and transferred to nitrocellulose or PVDF membranes. The membranes were immunoblotted with antibodies against each protein of interest (see Supplementary Methods). After incubation with secondary antibodies (IRDye 800 goat anti-rabbit or Alexa Fluor 680 goat anti-mouse), proteins were visualized and quantified using an Odyssey infrared imaging system (LI-COR Biosciences). To quantify O-GlcNAc stoichiometries, the intensities of the PEG-shifted band (glycosylated protein fraction) and the unshifted band (non-glycosylated protein fraction) were measured using Odyssey imaging software (Version 2.1). The resulting values of the PEG-shifted bands were corrected for non-specific background by subtracting the background intensity from negative control reactions. For data and statistical analyses, mean values, standard error of the mean, and P-values (paired, two-tailed, Student’s T-tests, α-value = 0.05) were calculated using the program Excel.
Publication 2010
Adult Animals Animals, Laboratory Antibodies Bistris Brain Cells Cortex, Cerebral Cultured Cells Cytosol Detergents Embryo Gels Glycosylated Proteins Goat HEK293 Cells Hypothalamus Institutional Animal Care and Use Committees IRDye800 Liver MECP2 protein, human Mus N-acetylglucosaminono-1,5-lactone O-(phenylcarbamoyl)oxime Neurons Nitrocellulose Pellets, Drug polyvinylidene fluoride Protein Glycosylation Proteins Rabbits Rats, Sprague-Dawley Seahorses Sf9 Cells Student Synapsins Tissue, Membrane

Most recents protocols related to «IRDye800»

The ROs were pooled (10) and lysed in radioimmunoprecipitation assay protein lysis buffer (Abcam) with protease inhibitor cocktail (Roche, Basel, Switzerland) and homogenized using a 25G needle. The protein concentration was assessed using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions and the plate absorbance was read in the SpectraMAX plate reader (Molecular Devices, San Jose, CA, USA) at 562 nm. The samples (22.5–85 μg) were loaded on 4–20% Mini-PROTEAN TGX Precast Protein Gels (Bio-Rad), ran for the first 30 min at 70 V and the next 4 h at 100 V in Tris-Glycine SDS buffer. The gels were transferred to PVDF membranes (Merck KGaA) previously activated with methanol, in 1× Tris-Glycine buffer and 20% methanol at 70 mV overnight at 4°C. The membranes were rinsed in PBS-0.1% Tween, blocked in Pure Odyssey Blocking Buffer (Li-COR Biosciences, Lincoln, NE, USA) for 2 h and incubated with an anti-ABCA4 clone 5B4 (1:1,000; Merck KGaA) and anti-vinculin (1:5,000; Abcam) at 4°C overnight. The membranes were washed with PBS-0.1% Tween and incubated with Goat Anti-Mouse IRDye 800 and Goat Anti-Rabbit IRDye 680 (1:5000; Li-COR Biosciences) for 1.5 h in the dark. The membranes were washed with PBS-0.1% Tween and scanned wet in the Odyssey IR system (Li-COR Biosciences). The intensity of the detected bands was quantified using FIJI ImageJ 1.53c, and the samples were normalized to the wild-type sample. The mean percentage of the detected ABCA4 protein was statistically analyzed using GraphPad Prism 9, with ordinary one-way ANOVA test followed by Dunnet’s multiple comparison test.
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Publication 2023
Biological Assay Buffers Clone Cells Gels Glycine Goat IRDye800 Medical Devices Methanol Mice, House Needles neuro-oncological ventral antigen 2, human polyvinylidene fluoride prisma Protease Inhibitors Proteins Rabbits Radioimmunoprecipitation Assay Tissue, Membrane Tromethamine Tweens Vinculin
Cells were lysed in RIPA buffer (50 mM Tris–HCl, pH 7.5, 0.5% DOC, 0.1% SDS, 1% NP-40, and 150 mM NaCl) with protease and phosphatase inhibitors (#4693159001 and #4906837001; Roche), followed by sonication at the highest setting with a pulse of ± 30 s. After centrifugation at 16,000g for 30 min, lysates were collected in a fresh tube and protein concentration was determined using BCA assay (Pierce). 6× loading buffer was added to lysates, and they were boiled at 95°C for 10 min. Equal amounts of lysates were loaded on 4–20% precast gradient gels (Bio-Rad) and separated at 80–100 V. Proteins were blotted using PVDF membrane (Bio-Rad) and blocked for 1 h at RT. Membranes were incubated overnight with primary antibody followed by washing. For detection, HRP-labeled secondary antibodies (DAKO) followed by incubation with Pierce ECL Western Blotting Substrate (Thermo Fisher Scientific) were used, or LI-COR Biosciences secondary antibodies (IRDye 680 or IRDye 800) were used followed by detection by Odyssey Imaging Systems or Bio-Rad Laboratories ChemiDoc Imaging Systems.
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Publication 2023
Antibodies Biological Assay Buffers Cells Centrifugation Gels Immunoglobulins inhibitors IRDye800 Nonidet P-40 Peptide Hydrolases Phosphoric Monoester Hydrolases polyvinylidene fluoride Proteins Pulse Rate Radioimmunoprecipitation Assay Sodium Chloride Tissue, Membrane Tromethamine
Fluorescently tagged and untagged DNA and RNA oligonucleotides were synthesized by Integrated DNA Technologies (IDT, IA). The sequences of oligonucleotides used in this study are listed in Table 1 and Supplemental Table 1. DNA and RNA probes were tagged on the 5’ end with an IRDye 800 fluorescent tag (LI-Cor, NE) or an Alexa Fluor 488, respectively. Double-stranded DNA (dsDNA) probes and competitors were produced from pairs of separately-synthesized complimentary oligonucleotides by mixing equal molar concentrations, heating to 95°C, and slowly cooling to room temperature.
EMSAs were performed as previously described [1 (link),4 (link)]. Unless stated otherwise, purified proteins were added to 100nM of labeled nucleic acid probes and incubated at room temperature for 5–15 minutes. Unlabeled nucleic acid competitors were added prior to the addition of protein. EGTA was added to the indicated reactions to inhibit RNAse activity in protein aliquots. Poly-dI-dC was added to indicated gels as a non-specific competitor. One-sixth volume of EMSA loading dye (15mg/mL Ficol 400, 0.8 mg/mL Orange G) was added. Electrophoresis was performed using pre-run 6% TBE gels (Invitrogen, MA) at 100-volts in 0.5x TBE buffer. Gels were imaged and analyzed via densitometry with a ChemiDoc MP and Image-Lab software, respectively (Bio-Rad, CA). Lanes and bands were added manually according to the strongest free probe and the strongest shifted band. Equivalent bands were then added across the entire EMSA.’ Background noise was calculated and accounted for by the Image-Lab software. Percent shifted was graphed using GraphPad Prism 9 (Dotmatics, MA).
Publication Preprint 2023
alexa fluor 488 Cardiac Arrest Densitometry DNA, Double-Stranded Egtazic Acid Electrophoresis Electrophoretic Mobility Shift Assay Gels IRDye800 Molar Nucleic Acid Probes Nucleic Acids Oligonucleotides Orange G poly(dC) prisma Proteins Ribonucleases RNA Probes Tris-borate-EDTA buffer
Mouse plasma samples (preheparin and postheparin) were incubated with magnetic beads coated with Ab3174. After removing unbound material, the immune precipitates were size-fractioned on a 4 to 12% Bis-Tris SDS–polyacrylamide gel for western blotting. Mouse LPL was detected with IRDye800-Ab3174. In separate studies, we incubated purified mouse LPL, purified mouse GPIHBP1, or LPL–GPIHBP1 complexes with magnetic beads coated with Ab3174. Immune precipitates were analyzed by western blotting with IRDye800-Ab3174 and IRDye680-11A12.
Publication 2023
Bistris Immune Precipitates IRDye800 Mus Plasma polyacrylamide gels
The margination of TRLs in blood vessels was measured as described previously (31 (link)). Briefly, TRLs were isolated from the plasma of Gpihbp1–/– mice by ultracentrifugation (d < 1.006 g/mL). Mice were injected intravenously with IRDye680-TRLs and IRDye800-2H8 in saline containing 0.25 mM tetrahydrolipstatin. After 60 s, mice were perfused with 20 mL PBS through the left ventricle, followed by 10 mL 3% PFA in PBS. Tissues were embedded in OCT; 10-μm-thick frozen sections were prepared (6 sections/tissue/mouse) and scanned using an infrared scanner. The TRL signal was normalized to the 2H8 signal.
Publication 2023
Blood Vessel Frozen Sections IRDye800 Left Ventricles Mus Orlistat Plasma Saline Solution Tissues Ultracentrifugation

Top products related to «IRDye800»

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IRDye 800 is a near-infrared fluorescent dye developed by LI-COR for use in a variety of analytical and imaging applications. It exhibits strong absorption and emission in the 800 nm wavelength range, making it suitable for detection in the near-infrared region of the spectrum.
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Odyssey Blocking Buffer is a protein-based solution designed for use in immunoblotting and Western blotting applications. It is formulated to effectively block non-specific binding of antibodies, thus improving the signal-to-noise ratio in these types of experiments.
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The Odyssey Imaging System is a fluorescence-based imager designed for detection and quantification of proteins and nucleic acids. It utilizes two near-infrared fluorescent dyes to enable multiplex detection and analysis. The system can be used for a variety of applications, including Western blotting, gel and membrane-based assays, and microplate-based assays.
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IRDye 680 is a near-infrared fluorescent dye used for labeling and detection applications in various scientific and analytical techniques. It has an excitation maximum at 680 nm and an emission maximum at 700 nm, making it suitable for use with near-infrared imaging systems.
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IRDye 800 is a near-infrared fluorescent dye used in various laboratory applications. It has an absorption and emission spectrum that allows for detection in the near-infrared range. The dye can be conjugated to various biomolecules, such as proteins, antibodies, and small molecules, to facilitate their detection and visualization in research and analytical procedures.
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More about "IRDye800"

IRDye800 is a near-infrared fluorescent dye commonly utilized in biomedical research and clinical applications.
It features a long excitation and emission wavelength range, enabling deep tissue imaging and reduced autofluorescence.
This makes IRDye800 a powerful tool for a variety of applications, including fluorescence imaging, molecular targeting, and surgical guidance.
The Odyssey Infrared Imaging System and Odyssey infrared scanner are popular platforms for detecting and analyzing IRDye800 signals.
These systems provide high-sensitivity detection and quantification of near-infrared fluorescent signals, allowing researchers to visualize and track biomarkers labeled with IRDye800 or other near-infrared dyes like IRDye 680 and Alexa Fluor 680.
Complementary products like Odyssey blocking buffer and PVDF membranes can be used in conjunction with IRDye800 experiments to optimize signal detection and reduce background noise, ensuring accurate and reproducible results.
PubCompare.ai's advanced AI-driven protocol analysis tools help researchers streamline their IRDye800 experiments by identifying the most reliable and effective methods from the scientific literature, preprints, and patents.
This allows researchers to save time, enhance the quality of their studies, and achieve superior IRDye800 research outcomes.