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6xmassruler dna loading dye

Manufactured by Thermo Fisher Scientific
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The 6xMassRuler DNA Loading Dye is a pre-mixed solution designed for use in gel electrophoresis. It is used to prepare DNA samples for loading into agarose or polyacrylamide gels, facilitating the visualization and tracking of DNA fragments during the electrophoresis process.

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Lab products found in correlation

Wizard genomic dna purification, by Promega (2 mentions) Typhoon phosphorimager, by GE Healthcare (2 mentions) Gelred nucleic acid stain, by Biotium (1 mentions) Massruler dna ladder, by Thermo Fisher Scientific (1 mentions) Gel doc xr system, by Bio-Rad (1 mentions) Image lab software, by Bio-Rad (1 mentions)

5 protocols using 6xmassruler dna loading dye

1

Agarose Gel Analysis of AuNP-Nucleic Acid Conjugates

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Agarose gel electrophoresis was used for three different concentrations of each AuNP-ssRNA, AuNP-dsRNA, AuNP-ssDNA, and AuNP-dsDNA conjugates. For this purpose, 2% w/v agarose (Sigma Aldrich, Prague, Czech Republic) containing GelRed™ nucleic acid stain (Biotium, California, USA), in Tris–acetate-EDTA buffer (TAE) was used and the gel ran under voltage of 110 V for 40 min. 5 µL of each sample was added to the wells after mixing with 1 µL of 6X MassRuler DNA loading dye (Thermo Fisher Scientific, Massachusetts, USA). Controls were MassRuler DNA ladder (Thermo Fisher Scientific, Prague, Czech Republic), AuNP, and four different free (non-conjugated) NAs: ssRNA, dsRNA, ssDNA, and dsDNA. When the NAs were conjugated to the AuNP, there was a migration delay in the conjugates in contrast to the control. The delayed migration of the NAs proves the successful conjugation51 (link),52 (link).
Pourali P., Dzmitruk V., Benada O., Svoboda M, & Benson V. (2023). Conjugation of microbial-derived gold nanoparticles to different types of nucleic acids: evaluation of transfection efficiency. Scientific Reports, 13, 14669.
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2

Isolation and Analysis of Telomeric DNA

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HeLa genomic DNA was isolated with the Wizard Genomic DNA purification according to the manufacturer’s instructions (Promega). 6 μg of genomic DNA was digested with 30U of HinfI and RsaI overnight at 37°C. The digested DNA was mixed with 6xMassRuler DNA Loading Dye (Thermo Fisher Scientific), loaded on a 0.8% agarose gel in 1xTBE and fractionated by gel electrophoresis at 2V/cm for 20 hours. The gels were dried for two hours at 50°C in vacuum, treated with denaturation buffer (0.5 M NaOH, 1.5 M NaCl) and neutralization buffer (0.5 M Tris-HCl pH 7.5, 1.5 M NaCl), followed by pre-hybridization with Church buffer for 1 hour at 50°C. The gels were hybridized overnight at 50°C with a randomly labeled TeloC probe as described previously23 . The gels were washed for 1 hour at 50°C with 4xSSC, 4xSSC 0.1%SDS, and 2xSSC 0.1%SDS, exposed to a phosphorimager screen and analyzed on a Typhoon phosphorimager (GE).
Feretzaki M., Pospíšilová M., Fernandes R.V., Lunardi T., Krejci L, & Lingner J. (2020). RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature, 587(7833), 303-308.
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3

Isolation and Analysis of Telomeric DNA

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HeLa genomic DNA was isolated with the Wizard Genomic DNA purification according to the manufacturer’s instructions (Promega). 6 μg of genomic DNA was digested with 30U of HinfI and RsaI overnight at 37°C. The digested DNA was mixed with 6xMassRuler DNA Loading Dye (Thermo Fisher Scientific), loaded on a 0.8% agarose gel in 1xTBE and fractionated by gel electrophoresis at 2V/cm for 20 hours. The gels were dried for two hours at 50°C in vacuum, treated with denaturation buffer (0.5 M NaOH, 1.5 M NaCl) and neutralization buffer (0.5 M Tris-HCl pH 7.5, 1.5 M NaCl), followed by pre-hybridization with Church buffer for 1 hour at 50°C. The gels were hybridized overnight at 50°C with a randomly labeled TeloC probe as described previously23 . The gels were washed for 1 hour at 50°C with 4xSSC, 4xSSC 0.1%SDS, and 2xSSC 0.1%SDS, exposed to a phosphorimager screen and analyzed on a Typhoon phosphorimager (GE).
Feretzaki M., Pospíšilová M., Fernandes R.V., Lunardi T., Krejci L, & Lingner J. (2020). RAD51-dependent recruitment of TERRA lncRNA to telomeres through R-loops. Nature, 587(7833), 303-308.
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4

Assessing Absence of Genetic Material in CMVs

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The absence of genetic material in the cell membrane suspension and in the final CMVs was assessed by 1% w/v agarose gel electrophoresis in TBE buffer. The membrane pellet isolated as described above was hydrated with the appropriate volume of starting buffer, vortexed and sonicated until suspended, then mixed with 6X MassRuler DNA Loading Dye (Thermo Fisher Scientific). To verify the absence of nucleic acids inside the final CMVs undergone the complete preparation procedure, an aliquot of CMVs was disrupted by ultrasounds, before mixing with 6X MassRuler DNA Loading Dye (Sigma). Electrophoresis was run at 80 V for 30 min, with an aliquot of the parent cell homogenate as positive control.
Balboni A., Ailuno G., Baldassari S., Drava G., Petretto A., Grinovero N., Cavalleri O., Angeli E., Lagomarsino A., Canepa P., Corsaro A., Tremonti B., Barbieri F., Thellung S., Contini P., Cortese K., Florio T, & Caviglioli G. (2024). Human glioblastoma-derived cell membrane nanovesicles: a novel, cell-specific strategy for boron neutron capture therapy of brain tumors. Scientific reports, 14(1).
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5

Quantifying dsGFP-Protein Binding Ratios

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Ten pmol of dsGFP was mixed with various amounts of protein, yielding molar ratios of protein/dsRNA of 5/1, 7:1, 10/1 and 20/1. Mixtures were incubated at room temperature for 15 minutes. After adding loading buffer (6x MassRuler DNA loading dye, Thermo Scientific), the entire sample was loaded on a 1.5% agarose gel in 0.5x TAE. Electrophoresis was performed at 100 V for 30' in 0.5x TAE running buffer. Gels were stained in an aqueous ethidium bromide solution (0.5 mg/l) for 15 min at room temperature and visualized using a GelDoc XR+ system with Image Lab software (Bio-Rad, Hercules, CA).
Martinez Z., De Schutter K., Van Damme E.J.M., Vogel E., Wynant N., Vanden Broeck J., Christiaens O, & Smagghe G. (2021). Accelerated delivery of dsRNA in lepidopteran midgut cells by a Galanthus nivalis lectin (GNA)-dsRNA-binding domain fusion protein. Pesticide biochemistry and physiology, 175.
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