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PRODAN is a fluorescent dye used in molecular biology applications. It is designed to detect and quantify the presence of specific biomolecules in samples. The core function of PRODAN is to serve as a labeling agent for analytical techniques such as fluorescence spectroscopy and microscopy.

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6 protocols using prodan

1

Determining CMC of Micelle Nanoparticles

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CMC of micelle-based nanoparticles composed of p(DMAEMA)-b-p(DMAEMA-co-BMA-co-PAA) was approximated using solvatochromic shifts in fluorescence emission of PRODAN® (Molecular Probes, Eugene, Oregon).81 (link), 82 Briefly, PRODAN® dissolved in methanol was aliquoted into black 96-well plates. After drying overnight, micelle solutions at a range of concentrations (0–2 mg/ml) were added and incubated overnight to achieve final PRODAN® concentrations of 5.45*10−4 mg/ml. PRODAN® emission was measured at two wavelengths (Ex/Em1: 360 nm/436 nm and Ex/Em2: 360 nm/518 nm) that corresponds to emission of PRODAN® in hydrophobic and hydrophilic phases, respectively. The ratio of emissions (hydrophobic phase/hydrophilic phase, Em1/Em2) was plotted versus of log(micelle concentration), and CMC was determined as a concentration at which the emission ratio begins to increase with polymer concentration (Supplemental Figure S1).
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2

Evaluating Schisandra Sphenanthera Compounds

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Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS), L-glutamine, non-essential amino acids (NAAs), streptomycin and penicillin from GIBCO-Invitrogen (Carlsbad, CA), heparin, bafilomycin A1, NH4Cl, 2-Oleoyl-1-palmitoyl-sn-glycero-3-phospho-choline (POPC) and cholesterol from Sigma-Aldrich Corporation (St Louis, MO) and 4′,6-diamidino-2-phenylindole (DAPI) from Invitrogen (Carlsbad, CA) were used in this study. HCV NS3-4A serine protease inhibitor telaprevir, NS5A inhibitor dasatinib, HCV assembly inhibitor naringenin and (-)-epigallocatechin gallate (EGCG) were purchased from Selleck Chemicals (Houston, TX). Fluorescent dye Prodan was from Molecular Probes (Invitrogen, Carlsbad, CA). SZA and other natural compounds were extracted and isolated from the fruits of Schisandra sphenanthera Rehd. et Wils. as previously described30 . The schisandra fruits were collected in Yunnan province and identified as dry fruits by professor Han-Ming Zhang. For the detailed procedures (see Supplementary materials and methods).
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3

Synthesis and Characterization of Peptides and Lipids

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Peptides SS-31 and SS-20 were prepared by solid-phase synthesis by Phoenix Pharmaceuticals (Burlingame, CA), and [ald]SS-31 was synthesized as described (12 (link)). All peptides were prepared as aqueous stocks. Synthetic phospholipids were purchased as chloroform stocks from Avanti Polar Lipids (Alabaster, AL), including POPC, POPG, and variants of cardiolipin with 18:1 acyl chains, including TOCL and trioleoyl MLCL. All lipid stocks were stored at −20 °C in clear vials with Teflon-lined cap closures until use. Fluorescent probes TMRM, laurdan, prodan, DPH, ANS, and CG-5N were purchased from Molecular Probes (Thermo Fisher Scientific). Solutions were prepared with deionized ultrapure water, and all buffers, salts and other reagents were obtained from Sigma–Aldrich.
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4

Comparative Lipid and Phospholipidosis Assays

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General chemicals were from VWR (West Chester, PA). Nile Red and Oil Red O (ORO) were from EMD (Gibbstown, NJ). Filipin was from Sigma (St Louis, MO). LipidTOX dyes and Red Phospholipidosis Detection Reagent (LipidTox-PDR, H34351) were from Molecular Probes (Eugene, OR). 4′,6-diamidino-2-phenylindole (DAPI), and concanavalin A were from Invitrogen (Temecula, CA). Alexa- and horseradish peroxidase (HRP)-conjugated secondary antibodies were from Amersham (Piscataway, NJ). Laurdan, Prodan, 7-aminoactinomycin D (7-AAD), and diphenylhexatriene (DPH) were from Molecular Probes. The Toll-Like Receptor (TLR) ligands peptidoglycan (PGN) from Staphylococcus aureus, synthetic triacylated lipoprotein (Pam3CSK4), and standard lipopolysaccharide (LPS) from Escherichia coli were from Sigma. Phospholipidosis-inducing drugs were sourced as follows: acetaminophen, cyclosporin A (CsA) and propranolol hydrochloride from Sigma (St Louis, MO), and chlorcyclizine hydrochloride from MP Biomedicals (Santa Ana, CA). Anti-PPARγ and anti-TLR antibody were each from Abcam (Cambridge, MA). Anti-GRB2 (loading control) was from Cell Signalling Technologies (Danvers, MA).
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5

Evaluating Micelle-based Nanoparticle Carriers

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CMC of micelle-based nanoparticle carriers (NPC) composed of p(DMAEMA)-b-p(DMAEMA-co-BMA-co-PAA) was approximated using solvatochromic shifts in fluorescence emission of PRODAN® (Molecular Probes, Eugene, Oregon)50 (link), 51 (link). Briefly, PRODAN® dissolved in methanol was aliquoted into black 96-well plates. After drying overnight, micelle solutions at a range of concentrations (0–2 mg/ml) were added and incubated overnight to achieve final PRODAN® concentrations of 5.45*10−4 mg/ml. PRODAN® emission was measured at two wavelengths (Ex/Em1: 360 nm/436 nm and Ex/Em2: 360 nm/518 nm) that corresponds to emission of PRODAN® in hydrophobic and hydrophilic phases, respectively. The ratio of emissions (hydrophobic phase/hydrophilic phase, Em1/Em2) was plotted versus of log(micelle concentration), and CMC was determined as a concentration at which the emission ratio begins to increase with polymer concentration.
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6

Determining NPC Critical Micelle Concentration

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NPC critical micelle concentration (CMC) was completed using fluorescence spectral emission shifts of 6-propionyl-2-(dimethylamino)naphthalene (PRODAN, Molecular Probes, Eugene, OR, USA) caused by partitioning differences into hydrophilic versus hydrophobic NPC regions, as described previously (38 (link), 39 , 47 (link)). PRODAN was dissolved in methanol at 24 μM, and 10 μL of this PRODAN solution was aliquoted into each well of a black 96-well plate. After drying overnight, a range of NPC solutions (0.5 ng/mL to 0.1 mg/mL) were diluted using 1X DPBS, and 100 μL/well of each sample solution was loaded into the 96-well plates containing PRODAN. All samples were loaded in triplicate, and plates were sealed and incubated at 4 °C overnight. PRODAN fluorescence was measured at two wavelengths (Ex/Em1: 360 nm/435 nm for hydrophilic detection and Ex/Em2: 360 nm/520 nm for hydrophobic detection) using a Tecan plate reader. The ratio of hydrophilic to hydrophobic emission (Em1/Em2) was plotted against the log10 polymer concentration, linear regression lines were applied to each phase of the graph, and the CMC was determined as the concentration at which these regression lines intersect (see Supplemental Figure S2).
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