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8 protocols using 12 mercaptododecanoic acid

1

Fabrication of Biosensor Prototype

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LC 4-cyano-4′-n-pentylbiphenyl (5CB) was purchased from Jiangsu Hecheng Display Technology Co., Ltd. (Nanjing, China). The EcoRI and BamHI restriction enzymes were purchased from the TaKaRa Biotech company (Dalian, China). Thrombin was purchased from J&K Scientific (Beijing, China). Poly(dimethyl siloxane) (PDMS) was purchased from Dow Corning (Midland, MI, USA). 12-mercaptododecanoic acid was purchased from Sigma (Burlington, MA, USA). Other chemicals were purchased from Tianjing Fuchen Chemical Reagents Factory (Tianjin, China). All DNA sequences are shown in Table S1, which were synthesized by Beijing Qingke Biological Technology Co., Ltd. (Beijing, China). Glass microscope slides (Fisher’s Finest Premium grade) were purchased from Fisher Scientific (Pittsburgh, PA, USA). The buffer solution used in this work was phosphate-buffered saline (PBS, pH 7.4, 2 mM KH2PO4, 8 mM Na2HPO4, 136 mM NaCl, and 2.6 mM KCl).
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2

Synthesis and Functionalization of Spherical Gold Nanoparticles

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Spherical GNPs (20nm) were synthesized using sodium citrate as a reducing agent, based on a well-established procedure 54 (link), 56 (link). GNPs were conjugated to MDDA linker (12-mercaptododecanoic acid, Sigma) then coated with D-(þ)-glucosamine hydrochloride (Sigma), due to its stability and high cell-uptake rate.
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3

Mineral Cleavage Surface Preparation

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Muscovite mica (Ted Pella) and goethite (Cornwall, UK) were used as received, and both minerals were freshly cleaved along (001) or (010) cleavage planes, respectively, prior to experiments. Sodium chloride (99.99%), calcium chloride (99.99%), sodium hydroxide, and hydrochloric acid (Sigma-Aldrich) were used as received. Molecules for tip functionalization of self assembled monolayers of 11-amino-1-undecanethiol hydrochloride (99%), 11-mercaptoundecylphosphoric acid (95%), 12-mercaptododecanoic acid (96%), 1,11-undecanethiol (99%) (Sigma-Aldrich) were used as received.
Solutions with varying pH were adjusted using NaOH and HCl, and all solutions were filtered through a 0.22 μm filter prior to performing experiments.
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4

Fabrication and Functionalization of Polymer-Coated Glass Beads

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Glass beads SPHERIGLASS® A-Glass 2429 (70–100 μm diameter) obtained from Potters Industries LLC. Acrylic acid (AA), ammonium persulfate (APS), 1,2-bis(trimethoxysilyl)ethane, glutaraldehyde (GA), phosphate buffered saline (PBS) tablets, N-isopropylacrylamide (NIPAM), N,N′-methylene-bisacrylamide (BIS), N-tertbutylacrylamide (TBAm), N,N,N′,N′-tetramethyl-ethylenediamine (TEMED), trypsin from bovine pancreas, glucose, glycine, sorbitol, trehalose, 12-mercaptododecanoic acid, acetone, ethanol, methanol and toluene were purchased from Sigma-Aldrich, UK. 3-Aminopropyltriethoxysilane and sodium cyanoborohydride were obtained from Acros Organics. N-(3-Aminopropyl) methacrylamide hydrochloride (NAPMA) was purchased from PolySciences Inc., UK. Acetonitrile (ACN), sodium hydroxide (NaOH) and sulphuric acid (H2SO4) were obtained from Fisher Scientific (UK). Ultrapure water was produced by a Millipore Milli-Q system (Millipore, Bedford, MA, USA). Double-distilled ultrapure water (Millipore) was used for analysis. All chemicals and solvents were analytical or HPLC grade and were used without further purification. Phosphate buffered saline (PBS) was prepared as directed from PBS buffer tablets (Sigma-Aldrich, Gillingham, UK). N-Fluorescein acrylate was provided by Leicester Biotechnology Group.
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5

Preparation of Self-Assembled Monolayers

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SAMs were prepared using a protocol modified from our previous study (15 (link)). Briefly, the Au surfaces (40 nm) were deposited on glass coverslips following a Ti layer (40 nm), using an ANELVAL-400EK electron beam evaporator (Canon Anelva Corp., Kanagawa, Japan). The silicon wafers coated with Au (Zhongding Ltd., Yangzhou, China) were washed with triple-distilled water in an ultrasonic bath for 10 min, and immersed in 1 Mm 1-undecanethiol (-CH3; Sigma, St. Louis, MO, USA), 11-amino-1-undecanethiol (-NH2; Sigma), 11-hydroxy-1-undecanethiol (-OH; Sigma), 12-mercaptododecanoic acid (-COOH; Sigma) for 12 h (16 (link)). Following the self-assembly process, the substrates were washed with triple-distilled water and dried with nitrogen.
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6

Synthesis and Functionalization of Gold Nanoparticles

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The linker MDDA (12-Mercaptododecanoic acid, Sigma-Aldrich) conjugates between the GNP and the barbiturate. One side of the MDDA chain (thiol) connects to the gold via semi-covalent bonding, while the other side of the MDDA chain, carboxylic acid, binds to the negatively charged oxygen of the barbiturate. To each solution of the various GNP sizes, MDDA was added in excessive amounts, and the mixture was stirred for another four hours. Following this step, the solutions were centrifuged in order to reach higher concentrations. Next, the activating agents EDC (1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide HCl, Thermo Scientific) and NHS (N-Hydroxysulfosuccinimide sodium salt, Chem-Impex International) were added to the mixture together with the barbiturate, and stirred overnight (Figure 8). The solutions were centrifuged again in order to increase concentration.

Synthesis of GNPs. Schematic diagram of the synthesis of GNPs and functionalization with barbiturate. In order to conjugate the glucosamine to the GNP, the linker 12-Mercaptododecanoic acid (MDDA) was utilized. EDC and NHS were added in order to activate the carboxylic acids of the linker. One side of the MDDA chain (thiol) connects to the gold via semi-covalent bonding, while the other side, carboxylic acid, binds to the negatively charged oxygen of the barbiturate.

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7

Nanomaterial Characterization Protocol

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Sodium phosphate dibasic heptahydrate (ACS
grade, 98.0–102.0%), sodium phosphate monobasic monohydrate
(ACS grade, 98.0–102.0%), sodium chloride (ACS grade, ≥99.0%),
11-mercaptoundecyl-N, N,N-trimethylammonium
bromide (HS(CH2)11N(CH3)3Br), Trizma base (NH2C(CH2OH)3,
≥99.8%), 12-mercaptododecanoic acid (HS (CH2)11COOH, 96%), 1-dodecanethiol (HS(CH2)11CH3, ≥98%), and 11-mercapto-1-undecanol (HS(CH2)11OH, ≥99%) were purchased from Sigma-Aldrich
(St. Louis, MO). N-hydroxysulfosuccinimide (NHS),
1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC),
and plain microscope slides (25 × 75 × 1 mm) were purchased
from ThermoFisher Scientific (Waltham, MA). CSG10/Au probes were purchased
from NT-MDT Spectrum Instruments (Moscow, Russia). Ethanol 200 proof
was purchased from Decon Labs. Inc. (King of Prussia, PA). All aqueous
solutions or buffers were prepared using purified water with a resistivity
of ≥18 MΩ·cm from a nanopure filtration system (Thermo
Scientific) and filtered using a 0.2 μm disposable bottle top
filter before use. AAV2 and AAV8 empty and full capsids were purchased
from Vigene Biosciences Inc., Rockville, MD. Full capsids contained
the GFP gene.
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8

MDCK Cell Culture and H1N1 Virus Propagation

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MDCK (Madin-Darby Canine Kidney Cells) were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific, Waltham, MA, USA) with 1% Penicillin/Streptomycin and 10% FBS (Thermo Fisher Scientific, Waltham, MA, USA) in the humidified atmosphere in 5% CO2 at 37 °C.
H1N1 (A/Netherlands/2009) was a kind gift from Prof. M Schmolke (University of Geneva) and it was reproduced in MDCK cells and titrated by immunocytochemistry assay.
Heptakis-(6-deoxy-6-iodo)-β-Cyclodextrin was purchased from AraChem (Tilburg, Netherlands) and dried under high vacuum for 48 h prior to use. 12-mercaptododecanoic acid was purchased from Sigma-Aldrich (St. Louis, MO, USA) and dried in the same way. Neu5Acα2-6Galβ1-4GlcNAc-β-ethylamine was purchased from Asparia Glycomics (Donostia, Spain). Maleimide-PEG8-CH2CH2COOH was purchased from PurePEG (San Diego, CA, USA). All the other chemicals were purchased from Sigma-Aldrich (St. Louis, MO, USA) as reagent grade and used without further purification.
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