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10 protocols using deoxyribonucleic acid

1

DNase Test for S. aureus Identification

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Plates were prepared with agarose medium consisting of tryptose (Oxoid, Thermo Scientific, Leicestershire, UK), deoxyribonucleic acid (Sigma, St. Louis, MO, USA), sodium chloride (VWR Chemicals, Monroeville, PA, USA) and agar. The pH of the medium was set at 7.3 ± 0.2 and autoclaved at 121 °C for 15 min.
The method was based on a previously published study [24 (link)]. From the S. aureus colonies grown in TSA medium at 37 °C overnight, each of the 18 strains was inoculated with a sterile loop on the surface of DNase agar. The plates were inverted and incubated at 37 °C for 18–24 h. After incubation, 1N of HCL was added to the surfaces of the plates.
S. aureus ATCC 25923 and S. saprophyticus ATCC 15305 were used as positive and negative controls, respectively.
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2

Isolation of Cellular Biomolecules

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Deoxyribonucleic acid from human placenta (D3035), actin from rabbit muscle (A2522), myosin calcium activated from rabbit muscle (M1636), glyceryl trioleate (T7140), cytidine (C4654) were purchased in Sigma-Aldrich and used without any purification in powder form.
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3

Transformation and Culture of U. maydis Strains

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The U. maydis strains used in this work (Table S3) derive from the lab strains AB33 [14 (link)], SG200 [7 (link)], and SG200-pit1∆ [23 (link)]. The cells were grown in complete medium (CM: 0.25% w/v cas-amino acids (Difco), 0.1% w/v yeast extract (Difco), 1.0% v/v vitamin solution, and 6.25% v/v salt solution from Holliday [24 ], 0.05% w/v deoxyribonucleic acid from herring sperm, and 0.15% w/v NH4NO3 adjusted to pH 7.0 with NaOH (Sigma Aldrich, Darmstadt, Germany) and supplemented with 1% glucose. The transformation of U. maydis protoplasts followed the protocol from [25 (link)]. The constructs were integrated using homologous recombination into the pep4 or upp3 locus, and the transformants were selected on the corresponding antibiotics (200 μg/mL hygromycin, 150 μg/mL nourseothricin, 2 μg/mL carboxin (Sigma Aldrich, Darmstadt, Germany)).
For fluorescence analysis with plate readers, the strains were grown overnight in CM-glucose, before shifting the cultures to nitrate minimal medium (NM)-glucose for the induction of filamentous growth in AB33. Hyphal growth was induced by changing the media to nitrate minimal medium (NM) supplemented with 1% glucose or arabinose. All strains were confirmed using Southern blot analysis [8 (link)] or genotyping PCR.
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4

Chitosan-DNA-Pectin Biomaterial Synthesis

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Chitosan (CS, 50,000 to 190,000 Da) with 76% deacetylation degree, deoxyribonucleic acid (DNA, sodium salt from salmon testes, 20 kDa) and pectin from citrus peel (PC, Mw = 9000) with galacturonic acid ≥74.0%, were purchased from Sigma-Aldrich®. Methylene blue (MB), dipotassium phosphate (K2HPO4), acetic acid (CH3COOH), phosphoric acid (H3PO4), hydrated sodium acetate (C2H3NaO2.3H2O), hydrochloric acid (HCl) and sodium hydroxide (NaOH) were purchased from Honeywell® Company. Potassium dihydrogen phosphate (KH2PO4) was purchased from M&B® Company. All reagents used were of analytical grade and all solutions were prepared with Milli-Q ultrapure water.
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5

Salmon DNA-Assisted Carbon Nanotube Dispersion

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The sodium salt of salmon testes deoxyribonucleic acid (DNA with a mean molecular weight of 1300 kDa, which corresponds to 2000 base pairs and an approximate length of 660 nm), sodium bromide (NaBr), hydrochloric acid (HCl) (for pH = 2 solution), borax (for pH = 9 solution) and poly(ethylene glycol) 10,000 (PEG) were from SIGMA. Potassium phosphate monobasic (for pH = 7 solution) and CTAB were from FLUKA. CMC of CTAB at 25 °C is 0.98 mM in water and 0.14 mM in the presence of 10 mM NaBr, according to Okuda et al. [35 (link)]. The multi-walled carbon nanotubes (MWNT) were from Nanostructured & Amorphous Materials Inc. (Houston, TX, USA). The used MWNTs were 94% pure, stock No. 1240XH and with an outer average diameter between 20 and 30 nm and length between 0.5 and 2 μm. Deionized water was used for the preparation of the diverse solutions.
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6

DNA Oligonucleotide Fabrication and Characterization

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Deionized water was supplied from a Millipore system, continuously controlled for 18 MΩ cm and < 10 ppm TOC (total organic content). PCR primers (forward and reverse) and oligonucleotides containing the encoded message were purchased from Integrated DNA Technologies (IDT) and received in lyophylised form after standard desalting. All oligonucleotides were resuspended in deionized water to obtain a 100 μm stock and kept at 4 °C. Deoxyribonucleic acid, low molecular weight from salmon sperm (CAS:100403-24-5), Polyethylene oxide (PEO, Mw 400,000 Da, CAS:25322-68-3), Polyvinyl alcohol (PVA, Mw 146,000–186,000 Da, CAS: 9002-89-5) and Polycaprolactone (PCL, Mw 45,000 Da) were purchased from Sigma-Aldrich in dry form. The crosslinker Glutaraldehyde Grade I at 70 % in water (CAS: 111-30-8) and the surfactant Triton X-100 were purchased from Sigma-Aldrich. The DNA gel stain SYBRSafe was purchased from Invitrogen (Thermo Fischer Scientific).
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7

Nucleoside Analysis Protocol

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Cytidine, 5-methylCytidine, BIS-TRIS propane, tris(hydroxymethyl)aminomethane (TRIS), H3PO4, HCl, formic acid, acetonitrile, and deoxyribonucleic acid from calf thymus were purchased from Sigma-Aldrich, Italia (Milan, Italy). All the nucleosides were prepared as 1 mmol/L stock solutions in Milli-Q gradewater (Millipore, Milford, MA, USA) and stored at −80°C until use.
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8

Escherichia coli DNA Extraction and Analysis

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Deoxyribonucleic acid, sodium salt, from Escherichia coli strain B; calf thymus DNA; incomplete Freund's adjuvant (IFA); proteinase K; lysozyme; and methylated BSA (mBSA) were purchased from Sigma-Aldrich (St Louis, MO). Novagen pig genomic DNA was purchased from MilliporeSigma (St Louis, MO). Genomic Maxi-tips, Genomic DNA Buffer sets, and RNase A were purchased from Qiagen (Germantown, MD). TE buffer, pH 8.0, was purchased from Amresco Life Science/VWR (Radnor, PA). A 200-bp DNA ladder (New England Biolabs), 96-well Maxisorp microplates, and T-PER (Tissue Protein Extraction Reagent) were purchased from New Thermo Scientific (Waltham, MA). Goat anti-mouse IgG (H + L) conjugated to horseradish peroxidase was purchased from Novus Biologicals (Littleton, CO). TMB substrate (BD OptEIA Reagent) was purchased from BD Biosciences (San Jose, CA). A ProcartaPlex Mouse Cytokine/Chemokine Panel 1A 36plex Kit was purchased from Invitrogen (Carlsbad, CA).
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9

Evaluating Anti-Biofilm Efficacy of AuNPs

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The impact of DNA, sodium chloride and magnesium ions on the anti-biofilm activity of AuNPs was quantitatively investigated by the estimation of ED50% preventive values. Briefly, LB broth medium was supplemented with deoxyribonucleic acid from salmon sperm, sodium chloride, or magnesium chloride (Sigma-Aldrich, Saint Louis, USA) to final concentrations of 1 mg/mL, 180 mM, and 1 mM, respectively, and biofilm viability assessment was performed as described.
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10

Characterization of DNA-Loaded Nanoparticles

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DNA (deoxyribonucleic acid, low molecular weight from salmon sperm, Sigma-Aldrich) was dissolved in phosphate buffered solution (PBS) to obtain a concentration of 1 mg/ml. Subsequently, 10 mg of NPs were dispersed in 1 mL of DNA solution and gently stirred for 2 h. The NPs were separated from the absorption solution by ultracentrifugation (Mikro 200 Hettich Zentrifugen, Tuttlingen, Germany) at 14 000 rpm for 15 min. A solution of DNA in PBS (1 mg/ml) was centrifuged in the same conditions and subsequently analyzed by high performance liquid chromatography (HPLC; Series 200; Perkin Elmer, Waltham, MA, USA) in order to verify the possible presence of pelleted DNA. Release tests were carried out by dispersing 10 mg of DNA-loaded NPs into 1 mL of PBS at 37°C. An aliquot of the release medium was collected at predetermined intervals, and fresh PBS was reinstated. Absorption and release tests were performed in triplicate both on the NSs and NCs. The collected samples were subsequently analyzed by HPLC.
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