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Molecular Probes

Molecular Probes are a class of fluorescent and luminescent reagents used to label and detect biomolecules in living cells and tissues.
These probes can be tailored to target specific proteins, nucleic acids, lipids, and other cellular components, enabling researchers to visualize and quantify a wide range of biological processes.
Molecular Probes offer high sensitivity, specificity, and versatility, revolutionizing life science research by providing powerful tools for imaging, flow cytometry, high-throughput screening, and more.
PubCompare.ai's AI-driven platform can help researchers optimize the use of Molecular Probes, streamlining experiments and maximizing results through intelligent comparisons of protocols from literature, pre-prints, and patents.
Experiance seamless protocol optimization and product selection today with PubCompare.ai's powerful AI-assisted platform.

Most cited protocols related to «Molecular Probes»

C. crescentus, B. subtilis, A. biprosthecum, Rhodomicrobium sp, and P. hirshii were grown in PYE14 (link) at 30°C. A. tumefaciens, S. venezuelae, L. lactis, were grown in LB15 (link) at 30°C and E. coli was grown in LB15 (link) at 37°C. M. xanthus were grown at 32°C in CYE16 (link). S. pneumonia were grown at 37°C in THY17 . Rhodopseudomonas palustris CGA009 was grown anaerobically in defined mineral medium (PM)18 supplemented with 10 mM succinate and incubated at 30°C with constant illumination from a 60 W incandescent light bulb.
Phase and fluorescence time-lapse imaging was performed on a Nikon Ti-E inverted microscope, equipped with a Plan Apo 60×, 1.40 NA, Oil, Ph3 DM objective and 1.5× magnifier. Images were acquired every 5 min, and fluorescent proteins were illuminated with a Lumencor Spectra × light engine equipped with excitation filters 470/24 (GFP), 510/25 (YFP) or 575/25 (mCherry), Chroma emission filters 510/40 (GFP), 545/30 (YFP), 530/60 (mCherry) and either a quad polychroic DAPI/FITC/Cy3/Cy5 or triple polychroic CFP/YFP/mCherry cube for Lumencor SpectraX. Images were acquired using an Andor iXon3 DU885 EM CCD camera driven by NIS Elements Advanced Research software (Nikon, Melville, NY)
Cultures from strain YB4667 CB15::pvan-ftsZ-yfp were grown in PYE medium at 30°C and induced for 2 hours with 0.5 mM vanillic acid to express FtsZ-YFP. Exponentially growing cells from this culture were spotted onto a 0.8 mm thick 1% agarose pad made with PYE medium containing 0.5 mM vanillic acid and timelapse images were acquired every 5 minutes from 16 different slide positions for 54 time points. For cell division inhibition, 30 µg/ml of cephalexin was added to the agarose pad during the imaging period.
For precision assessment of MicrobeJ, Molecular Probes FluoSpheres carboxylate-modified microspheres (F8823), 1± 0.0480 µm lot #1761288 were spotted onto a 1% agarose pad made with deionized water and images were acquired for 30 ms using the same microscope, camera and objective as cells.
Publication 2016
Apolipoproteins A Cell Culture Techniques Cells Cephalexin DAPI Division, Cell Escherichia coli Fluorescein-5-isothiocyanate Fluorescence Incandescence Light Medulla Oblongata Microscopy Microspheres Minerals Molecular Probes Pneumonia Proteins Psychological Inhibition Rhodomicrobium Rhodopseudomonas palustris Sepharose Strains Succinate Vanillic Acid
Four 9 month old male mice (C57Bl/SJL) were used. Animals were anesthetized with choral hydrate (15% aqueous solution, i.p.) and were perfused transcardially with 4% paraformaldehyde and 0.125% glutaraldehyde in phosphate buffer saline (PBS; pH 7.4). The brains were then carefully removed from the skull and postfixed for 6 hours. All procedures were conducted in accordance with the National Institute of Health Guide for the Care and Use of Laboratory Animals and were approved by the Mount Sinai School of Medicine Institutional Animal Care and Uses Committee.
For intracellular injections, brains were coronally sectioned at 200 µm on a Vibratome (Leica, Nussloch, Germany). The sections were then incubated in 4,6-diamidino-2-phenylindole (DAPI; Sigma, St. Louis, MO, USA), a fluorescent nucleic acid stain, for 5 minutes, mounted on nitrocellulose filter paper and immersed in PBS. Using DAPI as a staining guide, individual layer II/III pyramidal neurons of the frontal cortex were loaded with 5% Lucifer Yellow (Molecular Probes, Eugene, OR, USA) in distilled water under a DC current of 3–8 nA for 10 minutes, or until the dye had filled distal processes and no further loading was observed [45] (link), [49] (link). Tissue slices were then mounted and coverslipped in Permafluor. Dendritic segment and spine imaging was performed using a Zeiss 410 confocal laser scanning microscope (Zeiss, Thornwood, NY, USA) using a 488 nm excitation wavelength, using a 1.4 N.A. Plan-Apochromat 100× objective with a working distance of 170 µm and a 5× digital zoom. After gain and offset settings were optimized, segments were digitally imaged at 0.1 µm increments, along the optical axis. The confocal stacks were then deconvolved with AutoDeblur (MediaCybernetics, Bethesda, MD, USA).
Supporting Information is available online (Box S1)
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Publication 2008
Animals Animals, Laboratory Brain Buffers Cranium DAPI Dendrites Epistropheus Fingers Glutaral Lobe, Frontal lucifer yellow Males Mice, House Microscopy, Confocal Molecular Probes Nitrocellulose Nucleic Acids paraform Phosphates Protoplasm Pyramidal Cells Saline Solution Stains Tissues Vertebral Column Vision
For in situ hybridization analysis, cryostat sections were hybridized using digoxigenin-labeled probes [45 (link)] directed against mouse TrkA or TrkB, or rat TrkC (gift from L. F. Parada). Antibodies used in this study were as follows: rabbit anti-Er81 [14 (link)], rabbit anti-Pea3 [14 (link)], rabbit anti-PV [14 (link)], rabbit anti-eGFP (Molecular Probes, Eugene, Oregon, United States), rabbit anti-Calbindin, rabbit anti-Calretinin (Swant, Bellinzona, Switzerland), rabbit anti-CGRP (Chemicon, Temecula, California, United States), rabbit anti-vGlut1 (Synaptic Systems, Goettingen, Germany), rabbit anti-Brn3a (gift from E. Turner), rabbit anti-TrkA and -p75 (gift from L. F. Reichardt), rabbit anti-Runx3 (Kramer and Arber, unpublished reagent), rabbit anti-Rhodamine (Molecular Probes), mouse anti-neurofilament (American Type Culture Collection, Manassas, Virginia, United States), sheep anti-eGFP (Biogenesis, Poole, United Kingdom), goat anti-LacZ [14 (link)], goat anti-TrkC (gift from L. F. Reichardt), and guinea pig anti-Isl1 [14 (link)]. Terminal deoxynucleotidyl transferase-mediated biotinylated UTP nick end labeling (TUNEL) to detect apoptotic cells in E13.5 DRG on cryostat sections was performed as described by the manufacturer (Roche, Basel, Switzerland). Quantitative analysis of TUNEL+ DRG cells was performed essentially as described [27 (link)]. BrdU pulse-chase experiments and LacZ wholemount stainings were performed as previously described [46 (link)]. For anterograde tracing experiments to visualize projections of sensory neurons, rhodamine-conjugated dextran (Molecular Probes) was injected into single lumbar (L3) DRG at E13.5 or applied to whole lumbar dorsal roots (L3) at postnatal day (P) 5 using glass capillaries. After injection, animals were incubated for 2–3 h (E13.5) or overnight (P5). Cryostat sections were processed for immunohistochemistry as described [14 (link)] using fluorophore-conjugated secondary antibodies (1:1,000, Molecular Probes). Images were collected on an Olympus (Tokyo, Japan) confocal microscope. Images from in situ hybridization experiments were collected with an RT-SPOT camera (Diagnostic Instruments, Sterling Heights, Michigan, United States), and Corel (Eden Prairie, Minnesota, United States) Photo Paint 10.0 was used for digital processing of images.
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Publication 2005
Anabolism Animals Antibodies Apoptosis Bromodeoxyuridine Calbindins Calretinin Capillaries Cavia Cells Diagnosis Digoxigenin DNA Nucleotidylexotransferase Domestic Sheep Goat Immunohistochemistry In Situ Hybridization In Situ Nick-End Labeling LacZ Genes Lumbar Region Mice, House Microscopy, Confocal Molecular Probes Neurofilaments Neuron, Afferent Pulse Rate Rabbits Rhodamine rhodamine dextran Root, Dorsal Staining transcription factor PEA3 tropomyosin-related kinase-B, human
Postnatal P6 eyes were briefly fixed with 2% PFA in PBS at 4°C, then retinas were dissected and stored in methanol at -20°C. Immediately prior to staining retinas were re-fixed in 4% PFA for 20 minutes. PBS-washed retinas were stained with biotinylated isolectin B4 (Vectorlabs) followed by streptavidin-alexafluor 568 (Molecular Probes) and flat mounted for epifluorescence analysis on a CellR microscope (Olympus).
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Publication 2011
Eye Isolectins Methanol Microscopy Molecular Probes Retina Streptavidin
GM 12878 cells were stained with DAPI NucBlue Fixed Cell Stain (molecular probes) and live cells were sorted using a FACSAria (BD Biosciences) using a 100 μm nozzle. One peripheral blood sample (buffy coat) was stained with BD Bioscience antibodies CD14-A-488 (M5E2, 1:20), CD3-PE-Cy7 (SK7, 1:20), CD4-APC-Cy7 (RPA-T4, 1:20), and CD8 (RPA-T8, 1:20) for 20 minutes in the dark at RT. Cells were lysed using BDpharmLyse 1:10 dil in diH20 (BD) for 15 min, centrifuged for 5 minutes, washed with PBS 2% FBS X 2, and resuspended in PBS with 2% FBS. 50,000 CD3+CD8+, CD3+CD4+, and CD14+ cell populations were sorted into PBS with 10%FBS.
Publication 2013
Antibodies BLOOD Cells DAPI Molecular Probes Population Group

Most recents protocols related to «Molecular Probes»

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To determine where 2F2-grafted “humanized” antibodies and antibody variants are delivered upon internalization into the cell, colocalization studies of the anti-CD79b antibodies internalized into B-cell lines may be assessed in Ramos cell lines. LAMP-1 is a marker for late endosomes and lysosomes (Kleijmeer et al., Journal of Cell Biology, 139(3): 639-649 (1997); Hunziker et al., Bioessays, 18:379-389 (1996); Mellman et al., Annu. Rev. Dev. Biology, 12:575-625 (1996)), including MHC class II compartments (MIICs), which is a late endosome/lysosome-like compartment. HLA-DM is a marker for MIICs.

Ramos cells are incubated for 3 hours at 37° C. with 1 μg/ml 2F2-grafted “humanized” antibodies and antibody variants, FcR block (Miltenyi) and 25 μg/ml Alexa647-Transferrin (Molecular Probes) in complete carbonate-free medium (Gibco) with the presence of 10 μg/ml leupeptin (Roche) and 5 μM pepstatin (Roche) to inhibit lysosomal degradation. Cells are then washed twice, fixed with 3% paraformaldehyde (Electron Microscopy Sciences) for 20 minutes at room temperature, quenched with 50 mM NH4Cl (Sigma), permeabilized with 0.4% Saponin/2% FBS/1% BSA for 20 minutes and then incubated with 1 μg/ml Cy3 anti-mouse (Jackson Immunoresearch) for 20 minutes. The reaction is then blocked for 20 minutes with mouse IgG (Molecular Probes), followed by a 30 minute incubation with Image-iT FX Signal Enhancer (Molecular Probes). Cells are finally incubated with Zenon Alexa488-labeled mouse anti-LAMP1 (BD Pharmingen), a marker for both lysosomes and MIIC (a lysosome-like compartment that is part of the MHC class II pathway), for 20 minutes, and post-fixed with 3% PFA. Cells are resuspended in 20 μl saponin buffer and allowed to adhere to poly-lysine (Sigma) coated slides prior to mounting a coverglass with DAPI-containing VectaShield (Vector Laboratories). For immunofluorescence of the MIIC or lysosomes, cells are fixed, permeabilized and enhanced as above, then co-stained with Zenon labeled Alexa555-HLA-DM (BD Pharmingen) and Alexa488-Lamp1 in the presence of excess mouse IgG as per the manufacturer's instructions (Molecular Probes).

Accordingly, colocalization of 2F2-grafted “humanized” antibodies or antibody variants with MIIC or lysosomes of B-cell lines as assessed by immunofluorescence may indicate the molecules as excellent agents for therapy of tumors in mammals, including B-cell associated cancers, such as lymphomas (i.e. Non-Hodgkin's Lymphoma), leukemias (i.e. chronic lymphocytic leukemia), and other cancers of hematopoietic cells.

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Patent 2024
Alexa Fluor 647 Anti-Antibodies Antibodies, Monoclonal, Humanized B-Lymphocytes Buffers Carbonates CD79B protein, human Cell Lines Cells Chronic Lymphocytic Leukemia Cloning Vectors DAPI Electron Microscopy Endosomes Genes, MHC Class II Hematopoietic Neoplasms Immunofluorescence Immunoglobulins Leukemia leupeptin Lymphoma Lymphoma, Non-Hodgkin Lysine lysosomal-associated membrane protein 1, human Lysosomes Malignant Neoplasms Mammals Molecular Probes Mus Neoplasms paraform pepstatin Poly A Saponin Therapeutics Transferrin

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Publication 2023
Alexa Fluor 647 anti-IgG Antibodies Biological Assay Bos taurus Caseins Cloning Vectors Concanavalin A HEPES Immunoglobulins Lectin Mice, House Microarray Analysis Molecular Probes M protein, multiple myeloma polyhistidine Polysaccharides Proteins Saline Solution Serum Albumin Serum Albumin, Bovine Sodium Chloride Staphylococcal Protein A Streptavidin
96-well plates were coated with recombinant human IgG1.Fc (A42561; Invitrogen) or human LRP-1 Cluster II Fc Chimera Protein covering ∼10% of the full-length Lpr1 protein sequence, including 3 N-glycosylation sites (#2368-L2-050; R&D Systems) at 0.5 μg in 100 μl PBS, incubated at 4°C overnight, and blocked with 50 mg/ml BSA for 90 min at 30°C. Serial concentrations ranging from 0.1 to 3.2 μg of recombinant human GALECTIN-3 (#774408; Biolegend), and test agents were added in a total volume of 50 μl and then incubated for 4 h at 30°C. Wells were washed, fixed with 2% PFA in PBS for 15 min at room temperature, washed, and incubated with rat anti-mouse monoclonal galectin-3 antibody (#125401; Biolegend; clone M3/38, epitopes mapped within the N-terminal region) for 30 min on ice. After washing, wells were incubated with AF488-conjugated donkey anti-rat secondary antibody (A-21208; Invitrogen Molecular Probes) for 30 min on ice. After washing, fluorescence was determined using a SpectraMax L (Molecular Devices) plate reader (excitation 485, emission 538) to quantify galectin-3–Lrp1 binding.
Publication 2023
Amino Acid Sequence Antibodies, Anti-Idiotypic Chimera Clone Cells Epitopes Equus asinus Fluorescence Galectin 3 Homo sapiens IgG1 LGALS3 protein, human Medical Devices Mice, House Molecular Probes Monoclonal Antibodies NR4A2 protein, human Protein Glycosylation
Neurons were seeded on poly-L-lysine-coated #1.5 coverslips (633029; Carolina Biological Supply). At indicated timepoints, coverslips were briefly washed in Dulbecco’s PBS with calcium and magnesium (PBL02; Caisson Labs), and fixed for 15 min with 4% paraformaldehyde (diluted in PBS from 16%, Electron Microscopy Services, 15710) and 4% sucrose in PBS at 37°C. For immunolabeling of fascin, coverslips were washed and fixed for 10 min with ice-cold methanol at −20°C. Subsequent steps were performed at room temperature. Autofluorescence was quenched by incubation with 50 mM NH4Cl for 10 min at room temperature. Coverslips were blocked and permeabilized using a buffer of 10% goat serum and 0.1% Triton X-100 in PBS and incubating for 30 min. Antibodies were diluted in a buffer of 3% goat serum and 0.1% Triton X-100 in PBS. Coverslips were incubated with primary antibodies for 1 h, washed three times in PBS with 0.1% Tween-20, and incubated with secondary antibodies and Alexa Fluor 488 phalloidin (A12379; Thermo Fisher Scientific, 1:40) for 30 min. Coverslips were mounted using Prolong Gold Antifade (P36930; Thermo Fisher Scientific), and allowed to cure for at least 24 h prior to imaging. Antibodies used were as follows: mouse monoclonal anti-Arp2/3 complex (#MABT95; Millipore, RRID:AB_11205567; 1:250), mouse monoclonal anti-fascin (#54545; Cell Signaling Technology, RRID:AB_2799464; 1:50), rabbit monoclonal anti-β-III-tubulin (#5568; Cell Signaling, Clone D71G9, RRID:AB_10694505; 1:100), rabbit monoclonal anti-MAP2 (#8707; Cell Signaling, Clone D5G1, RRID:AB_2722660; 1:500), goat anti-rabbit Alexa Fluor 568 (#A-11011; Molecular Probes, RRID:AB_143157; 1:1,000), goat anti-rabbit Alexa Fluor 647 (#A-21245; Thermo Fisher Scientific, RRID:AB_2535813; 1:1,000).
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Publication 2023
Actin-Related Protein 2-3 Complex alexa 568 alexa fluor 488 Alexa Fluor 647 Antibodies Biopharmaceuticals Buffers Calcium Clone Cells Cold Temperature Electron Microscopy fascin Goat Gold Lysine Magnesium MAP2 protein, human Methanol Molecular Probes Mus Neurons paraform Phalloidine Poly-5 Rabbits Serum Sucrose Triton X-100 Tubulin Tween 20
For immunofluorescence experiments, different fixation methods were exploited depending on the antibodies used. For immunocytochemistry of MTs, cells were extracted for 1 min in prewarmed extraction buffer (0.3% Triton X-100 and 0.1% glutaraldehyde in MRB80 buffer (MRB80 buffer: 80 mM Pipes, 1 mM EGTA, and 4 mM MgCl2, pH 6.8) and subsequently fixed in prewarmed 4% PFA in PBS for 10 min. For immunocytochemistry of cytochrome C, cells were fixed in prewarmed 4% PFA in PBS for 10 min. For immunocytochemistry of EB1 and detyrosinated MTs, cells were fixed in ice-cold methanol for 10 min. Samples prepared for STED imaging were extracted for 1 min in pre-warmed extraction buffer (0.3% Triton X-100 and 0.1% glutaraldehyde in MRB80 buffer and subsequently fixed in prewarmed 4% PFA (15,170; Electron Microscopy Sciences) in MRB80 buffer for 10 min. After fixation, cells were washed with PBS, permeabilized with 0.25% Triton X-100 in PBS, washed again with PBS, and subsequently blocked for 1 h with 3% BSA in PBS. Cells were incubated with primary antibody diluted in 3% BSA in PBS for 1 h at RT, washed with PBS, and incubated with secondary antibody diluted in 3% BSA in PBS for 1 h at RT. Samples prepared for STED imaging were incubated for 2 h in primary and 2 h in secondary antibody. After washing with PBS, cells were dipped in MilliQ water, air-dried, and mounted on microscopy slides using Prolong Diamond (Molecular Probes). The following primary antibodies were used in this study: Cytochrome C (6H2.B4; BD Biosciences), EB1 (5/EB1 BD Biosciences), acetylated tubulin (6-11B-1; Sigma-Aldrich), α-tubulin (EP1332Y; Abcam), α-tubulin (B-5-1-2; Sigma-Aldrich), tyrosinated tubulin (YL1/2; Abcam), detyrosinated tubulin (AB3210; Merck), and GFP (GFP-1010; Aves Lab). DAPI (Molecular Probes) was used to visualize DNA.
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Publication 2023
alpha-Tubulin Antibodies Aves Buffers Cells Cold Temperature Cytochromes c DAPI Diamond Egtazic Acid Electron Microscopy Fluorescent Antibody Technique Glutaral Immunocytochemistry Immunoglobulins Magnesium Chloride Methanol Microscopy Molecular Probes piperazine-N,N'-bis(2-ethanesulfonic acid) Triton X-100 Tubulin

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DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.
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Alexa Fluor 488 is a fluorescent dye used in various biotechnological applications. It has an excitation maximum at 495 nm and an emission maximum at 519 nm, producing a green fluorescent signal. Alexa Fluor 488 is known for its brightness, photostability, and pH-insensitivity, making it a popular choice for labeling biomolecules in biological research.
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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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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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CFSE (Carboxyfluorescein succinimidyl ester) is a fluorescent dye used for cell proliferation and tracking assays. It binds to cellular proteins, allowing the labeling and monitoring of cell division in various cell types.
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Alexa 488 is a fluorescent dye used in various biological applications. It is a brighly fluorescent, green-emitting dye with excitation and emission maxima at 495 and 519 nm, respectively. Alexa 488 can be conjugated to biomolecules such as proteins, antibodies, or nucleic acids to enable their detection and visualization.
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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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ProLong Gold antifade reagent is a water-based mounting medium designed to retard the photobleaching of fluorophores in fluorescence microscopy applications. It is formulated to provide long-term preservation of fluorescent signals in fixed and immunolabeled samples.
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Fura-2 AM is a fluorescent calcium indicator used for measuring intracellular calcium levels. It is a cell-permeable derivative of the parent compound Fura-2. Fura-2 AM can be loaded into cells, where intracellular esterases cleave off the acetoxymethyl (AM) ester group, trapping the Fura-2 indicator inside the cell.
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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 "Molecular Probes"

Molecular Probes are a versatile class of fluorescent and luminescent reagents that are widely used in life science research to label and detect biomolecules within living cells and tissues.
These powerful tools, also known as fluorophores or fluorescent dyes, can be tailored to specifically target proteins, nucleic acids, lipids, and other cellular components, enabling researchers to visualize and quantify a wide range of biological processes.
The use of Molecular Probes has revolutionized fields such as imaging, flow cytometry, and high-throughput screening, providing scientists with unparalleled sensitivity, specificity, and versatility.
Commonly used Molecular Probes include DAPI (4',6-diamidino-2-phenylindole) for DNA staining, Alexa Fluor 488 and Alexa 488 for green fluorescence, Hoechst 33342 for nuclear labeling, CFSE (Carboxyfluorescein succinimidyl ester) for cell proliferation assays, and Fura-2 AM for calcium imaging.
In addition to these well-known Molecular Probes, researchers may also utilize Triton X-100 as a permeabilization agent, ProLong Gold antifade reagent to preserve fluorescent signals, and Bovine serum albumin (BSA) as a blocking agent to reduce non-specific binding.
PubCompare.ai's AI-driven platform can help researchers optimize the use of Molecular Probes, streamlining experiments and maximizing results through intelligent comparisons of protocols from literature, pre-prints, and patents.
By leveraging this powerful AI-assisted platform, scientists can experience seamless protocol optimization and product selection, leading to more efficient and effective research outcomes.