Agarose powder

Manufactured by Merck Group

Sourced in United States, United Kingdom

Agarose powder is a purified polysaccharide derived from red seaweed. It is a versatile and commonly used material in laboratories for the preparation of gels for various applications, such as electrophoresis and chromatography.

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Lab products found in correlation

24 protocols using agarose powder

Microneedle Penetration Capability Evaluation

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Scanning electron microscopy (SEM; Nova Nano SEM 450, FEI, Eindhoven, Netherlands) was performed to measure dimensions of etched microwell arrays after the 1st DRIE, as well as to characterize the structure of microneedle arrays after the 2nd DRIE. Also, to assess the penetration capability of microneedles, insertion forces to agarose gel tissue phantoms and a mouse brain were measured using a digital force gauge (M5-012E, Mark-10, Copiague, NY, USA) placed on a motorized test stand (ESM303E, Mark-10). The agarose gel phantoms were prepared in two different concentrations (0.5% and 1%) by mixing agarose powder (Sigma-Aldrich, St. Louis, MO, USA) in a phosphate buffered solution. It has been known that ~ 0.5% agarose gel mimics the compression mechanics of the brain [36 ] but we also doubled concentration (1%) of agarose gel to additionally verify the penetration capability of microneedles to a harder sample.
An adult mouse (C57BL/6 strain, 8 weeks old) was anesthetized by intraperitoneal injection of urethane (1.5 g kg⁻¹) and then euthanized by cervical dislocation for the acute experiment. The middle of the mouse head was shaved, and its skull was drilled to expose the brain surface. The animal experiment protocol was approved (KIST-2020-166) by Institutional Animal Care and Use Committees of KIST.

Roh H., Yoon Y.J., Park J.S., Kang D.H., Kwak S.M., Lee B.C, & Im M. (2021). Fabrication of High-Density Out-of-Plane Microneedle Arrays with Various Heights and Diverse Cross-Sectional Shapes. Nano-Micro Letters, 14, 24.

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Agarose Homogeneous and Line Phantoms

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A 1% agarose solution was prepared by mixing agarose powder (0.2 g, Sigma Aldrich, Poole UK) with deionized water (20 mL) at room temperature and heating to 90°C with constant stirring. Once all the agarose had dissolved, the temperature was reduced to 42°C. RO Beads were suspended in deionized water and progressively diluted to produce series of desired concentrations. Each dilution was mixed with an equal volume of agarose and a static uniform bead-agarose suspension was prepared by repeatedly withdrawing and expelling the solution using a manual pipette. This gelatinous suspension is generally referred to as a homogeneous phantom 14 (link). Line phantoms were similarly prepared except tubes of known inner diameters (0.28, 0.40, 0.58, 0.86 and 1.02 mm) were first filled with beads in deionized water prior to setting the filled tubes in an agarose matrix.

Duran R., Sharma K., Dreher M.R., Ashrafi K., Mirpour S., Lin M., Schernthaner R.E., Schlachter T.R., Tacher V., Lewis A.L., Willis S., den Hartog M., Radaelli A., Negussie A.H., Wood B.J, & Geschwind J.F. (2016). A Novel Inherently Radiopaque Bead for Transarterial Embolization to Treat Liver Cancer - A Pre-clinical Study. Theranostics, 6(1), 28-39.

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NSCLC Cell Line and PDO Characterization

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The A549, H1975, and HCC4006 NSCLC cell lines were purchased from ATCC (Manassas, VA, USA) and maintained as specified. CK7152 NSCLC PDO was obtained from NCI Patient-Derived Models Repository (PDMR). RPMI 1640 medium with L-glutamine, DMEM/F12 medium, trypsin-EDTA (0.25%), and 1X phosphate buffered saline (PBS) were purchased from Fisher Scientific (Waltham, MA, USA). Fetal bovine serum (FBS) was purchased from GeminiBio Inc. (West Sacramento, CA, USA). 100X antibiotic–antimycotic, calcein AM viability dye, and EpCAM monoclonal antibody were purchased from Invitrogen (Carlsbad, CA, USA). Agarose powder was purchased from Sigma-Aldrich (St. Louis, MO, USA). Propidium iodide was purchased from Alfa Aesar (Haverhill, MA, USA). Hoechst 33342 Solution was purchased from Thermo Fisher Scientific (Heretofore TFS, Waltham, MA, USA). Osimertinib and gefitinib were purchased from LC Laboratories (Woburn, MA, USA). The 10X blocking buffer, anti-MCM2 antibody, goat anti-mouse IgG H&L Alexa Fluor^® 488, goat anti-rabbit IgG H&L Alexa Fluor^® 647, Alexa Fluor^® 488 anti-EGFR (phospho Y1068) antibody, total anti-EGFR antibody. Anti-E-Cadherin antibody was purchased from Cell Signaling Technology (Danvers, MA, USA).

Luan Q., Becker J.H., Macaraniag C., Massad M.G., Zhou J., Shimamura T, & Papautsky I. (2022). Non-small cell lung carcinoma spheroid models in agarose microwells for drug response studies. Lab on a chip, 22(12), 2364-2375.

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3D Bioprinting with Agarose-Matrigel Hydrogel

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Agarose stock solution was prepared by dissolving agarose powder (Sigma) in DI-water at 2 wt% or 3 wt%, and then homogenized and sterilized by boiling. The stock solution was then stored in an incubator at 37°C. Matrigel (50 µg/ml) (Corning) was stored at −18°C and pre-warmed overnight at 4°C before experimental use. To produce a gel mixture for 3D printing, agarose stock solution was first poured into a tube (Cristalgen) that had been pre-warmed at 37°C. Matrigel was then added by continuously mixing with a sterilized spatula, followed by the addition of cell suspension (1 × 10⁸/ml). The gel mixture was homogenized by continuous stirring, and then transferred to the printing head of the 3D printer (Seraph Robotics) for printing or to the plate of a rheometer (Discovery Hybrid Rheometer, TA Instrument) for rheological testing.

Fan R., Piou M., Darling E., Cormier D., Sun J, & Wan J. (2016). Bio-printing cell-laden Matrigel–agarose constructs. Journal of biomaterials applications, 31(5), 684-692.

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HPV Multiplex Primer and Western Blot Analysis

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HPV multiplex primers, Agarose powder, Ethylenediaminetetraacetic acid (EDTA), 2- deoxyribonucleic acid (DNA) ladder and ethidium bromide were from Sigma-Aldrich (France). Tris-Base, glycine, sodium dodecyl sulfate, bis-acrylamide and nitrocellulose membrane, the protein ladder and the peroxidase conjugated secondary antibodies anti-rabbit and anti-mouse were purchased from Bio-Rad Inc (USA). Sodium chloride (NaCl), potassium chloride (KCl), Tween-20, protease inhibitor phenyl-methyl-sulfonyl fluoride (PMSF), 2-mercaptoethanol, methanol, glycerol, 1,4-Dithiothreitol (DTT), sodium fluoride (NaF), sodium azide (NaN₃), Tris-Hydrochloride (tris-HCl) and sodium dodecyl sulfate (SDS, NaC₁₂H₂₅SO₄) were from Sigma-Aldrich (USA). The primary antibody against lamin A/C was purchased from Transduction Lab (USA). Antibody against ß-tubulin was from Santa Cruz Biotechnology (CA, USA). The chemo-luminescence reagent “Super Signal West Dura Extended Duration Substrate” made by PIERCE was from Thermo Scientific (Rockford, IL USA) and was used on Western blot membranes for protein revelation after exposure to X-ray films [12 (link)].

Capo-chichi C.D., Aguida B., Chabi N.W., Acapko-Ezin J., Sossah-Hiffo J., Agossou V.K., Anagbla T., Zannou M., Houngbé F, & Sanni A. (2016). Diversity of high risk human papilloma viruses in women treated with antiretroviral and in healthy controls and discordance with cervical dysplasia in the South of Benin. Infectious Agents and Cancer, 11, 43.

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Graphite Oxide Reduction by Thermal Exfoliation

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To chemically exfoliate graphite, graphite oxides were prepared using the previously reported improved Hummer’s method [6 (link)]. Yellow-colored graphite oxide (6 g) and agarose powder (2.5 g, Sigma Aldrich, Burlington, VT, USA) were dispersed in 100 mL of deionized water to form Solution 1, which was ultrasonicated for 1 h to exfoliate graphite oxide, yielding a mixed solution of GO and agarose. The mixed solution was heated in a microwave oven for 1 min to completely dissolve the agarose powder, forming Solution 2, which was then poured onto a petri dish for cooling at room temperature. After cooling for 6 h, the GO-containing agarose gel was obtained, which was cut into pieces of the desired size and freeze-dried (Bondiro, Ilshinlab, Yangju, Korea) to sublimate the water inside the gel pores. The composite comprising the freeze-dried GO and agarose was subsequently calcined in air at 500 °C for 6 h to remove the agarose template and completely reduce GO to rGO.

Shin J., Park J.K., Kim G.W., Nam I, & Park S. (2022). Agarose Gel-Templating Synthesis of a 3D Wrinkled Graphene Architecture for Enhanced Supercapacitor Performance. Micromachines, 13(7), 1113.

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Phytochemical Extraction and Elucidation

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All organic solvents for the phytochemical extraction and elucidation (i.e., methanol (MeOH), ethyl acetate (EtOAc), dichloromethane (DCM), acetone, hexane, and dimethyl sulfoxide (DMSO)) and other chemical reagents (i.e., 3-(4,5-Dimethylthiazol 2-yl)-2,5-diphenyltetrazolium bromide (MTT), Hoechst 33342, propidium iodide (PI), crystal violet, formaldehyde, and agarose powder) were purchased from Sigma-Aldrich (St. Louis, MO, USA).

Jimoh T.O., Nuamnaichati N., Sungthong R., Chansriniyom C., Chanvorachote P., Likhitwitayawuid K., Chaotham C, & Sritularak B. (2022). Phytochemicals from Vanda bensonii and Their Bioactivities to Inhibit Growth and Metastasis of Non-Small Cell Lung Cancer Cells. Molecules, 27(22), 7902.

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Agarose Hydrogel Fabrication Protocol

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Agarose hydrogels (4%, w/v) were prepared by mixing and heating 4 g of agarose powder (low melting point, Sigma-Aldrich) in 100 mL deionized water until complete dissolution. The solution was then poured into cylindrical molds (9 mm diameter, 15 mm height) and allowed to cool to room temperature. Finally, the gel was covered with a droplet of water to avoid dehydration.

Capuana E., Marino D., Di Gesù R., La Carrubba V., Brucato V., Tuan R.S, & Gottardi R. (2021). A High-Throughput Mechanical Activator for Cartilage Engineering Enables Rapid Screening of in vitro Response of Tissue Models to Physiological and Supra-Physiological Loads. Cells, Tissues, Organs, 211(6), 670-688.

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Molecular Detection of SARS-CoV-2 and E. coli

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The PCR reagent of the SARS-CoV-2 was composed of 1× Premix Ex Taq HS (TaKaRa Biotechnology (Dalian) Co., Ltd., Dalian, China), 1× EvaGreen Dye (31000, Biotium, CA, USA), 500 nM of forward and reverse primers, and 104 to 106 copies per µL SARS-CoV-2 CDC positive plasmid (Sangon Biotech, Shanghai, China). Each test requires 20 µL of reagent and 15 µL mineral seal above that.
The PCR reagent of the Escherichia Coli was composed of 1× Premix Ex Taq HS, 250 nM of forward and reverse primers, and 1 × 105/mm³ of the suspension of Escherichia coli bacteria. Each test requires 20 µL of reagent and 15 µL mineral seal above that. The primer sequences were as Table 1.
Agarose powder (V900510, 2%, Sigma-Aldrich, St. Louis, MO, USA), DL2000 DNA marker (Jialan, Beijing, China), 0.5× TBE buffer (PH1755, Phygene Life Sciences Co., Ltd., Fuzhou, China), and Nucleic Acid GelStain (Gel-Green, KeyGEN Biotechnology, Nanjing, China) were used for agarose gel electrophoresis, which was detected at 302 nm with UV illuminator (ZF1-IIN, JIAPENG Co., Shanghai, China).

Wang K., Jiang Y., Guo Y., Geng M, & Wu W. (2022). An Optimized Thermal Feedback Methodology for Accurate Temperature Control and High Amplification Efficiency during Fluorescent qPCR. Bioengineering, 9(6), 237.

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Agarose Gel Electrophoresis for DNA Retention

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Agarose powder was obtained from Sigma Aldrich. Purified water with 18.2 MΩ resistivity (Milli-Q) was used in all cases. Gels were cast by heating a 0.5% w/v solution of agarose in 40 mM tris-acetate buffer (pH 7.2) until fully dissolved, then cast by cooling the solution to room temperature in an Owl B2 horizontal electrophoresis chamber with a centrally placed 20-well comb. The gel was submerged under 40 mM tris-acetate (pH 7.2) running buffer, samples were added to the wells, and the gel was run 90 minutes at 105 ± 3 volts. Gels were stained in 2.5 μg/mL ethidium bromide for 15 minutes at 37 °C, 50 rpm, and destained in Milli-Q water for 5 minutes at 37 °C, 50 rpm. Ethidium bromide-stained DNA was visualized using a UV trans-illuminator.
Gel images were analyzed by densitometry using ImageJ software38 . Lane profile plots were generated and integrated (data not shown). Using manual baselines, the control plasmid was set as 100% DNA migration. The inverse of the DNA migration in experimental wells relative to control DNA migration gave a measure of percent DNA retention. Results presented are the average of three gels.

Meisel J.W, & Gokel G.W. (2016). A Simplified Direct Lipid Mixing Lipoplex Preparation: Comparison of Liposomal-, Dimethylsulfoxide-, and Ethanol-Based Methods. Scientific Reports, 6, 27662.

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