Low range dna ladder

Manufactured by Thermo Fisher Scientific

Sourced in Germany

The Low Range DNA Ladder is a molecular weight marker used to determine the size of DNA fragments in agarose gel electrophoresis. It consists of a mixture of DNA fragments of known molecular weights, allowing for the estimation of the sizes of unknown DNA samples.

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Lab products found in correlation

Tritrack dna loading dye, by Thermo Fisher Scientific (1 mentions) Sybr gold nucleic acid gel stain, by Thermo Fisher Scientific (1 mentions) Chemidoc imaging system, by Bio-Rad (1 mentions) Loading buffer, by Thermo Fisher Scientific (1 mentions) Gelred staining, by Biotium (1 mentions) Taq dna polymerase kit, by Qiagen (1 mentions) Onestep ahead rt pcr kit, by Qiagen (1 mentions)

2 protocols using low range dna ladder

Quantitative PCR Analysis of mRNA and lncRNA

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To perform PCR, 2 µL of the above ligation mixture was mixed with various components for a final condition of 1× Q5 reaction buffer, 1× Q5 high GC enhancer, 200 µM of each dNTP, 0.5 µM forward and reverse primers, and 0.02 U/µL Q5 high-fidelity DNA polymerase (NEB, M0491L); the final PCR reaction volume was 35 µL. PCR was done for high abundance eEF1A1 mRNA and MALAT1 RNA sites at 15 cycles and for low abundance PSME2 and HPRT1 sites 25–35 cycles.
Half of the PCR mixture (17.5 µL) was mixed with 3.5 µL of 6× TriTrack DNA Loading Dye (ThermoFisher, R1161). The entire mixture was loaded on a prerun 10% nondenaturing gel containing 1× TBE, together with low range DNA ladder (ThermoFisher, SM1193). The gel was stained with SYBR gold nucleic acid gel stain (ThermoFisher, S11494) for 10 min. Product bands were visualized using the Bio-Rad ChemiDoc imaging system and the bands quantified using Image Lab.

Zhang W., Eckwahl M.J., Zhou K.I, & Pan T. (2019). Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA. RNA, 25(9), 1218-1225.

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Nested RT-PCR Detection of HEV ORF1

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Primers for nested RT-PCR, which amplify a 332 bp product from the HEV open reading frame 1 (ORF1) were designed by Johne et al. (2010 (link)). RNA from the HEV isolate 47832c (Johne et al. 2014 (link)) was used as positive control. For the first RT-PCR with a total reaction volume of 25 µl, 5 µl of template was amplified using the OneStep Ahead RT-PCR Kit (QIAGEN, Germany). Cycling profile included the following settings: 10 min at 50 °C, 5 min at 95 °C, 40 cycles of 10 s at 95 °C, 10 s at 55 °C, 10 s at 72 °C and 2 min at 72 °C. The second nested PCR was performed with 2 µl template from the first RT-PCR. The Taq DNA Polymerase Kit (QIAGEN, Germany) was used according to protocol in a total reaction volume of 50 µl. Primer concentrations were 0.3 µM and cycling conditions were the following: 3 min at 94 °C, 35 cycles of 45 s at 94 °C, 45 s at 60 °C, 1 min at 72 °C and 10 min at 72 °C.
PCR fragments were separated by gel electrophoresis on 1.5% agarose gels in 1 × TBE buffer with 10 µl of 10,000×g GelRed staining (Biotium, Germany) per 100 ml agarose solution. Loading buffer (Thermo Scientific, Germany) was mixed with the PCR products and gels were run for 50 min at 90 V. Low range DNA ladder (5 µl) was used as a size marker (Thermo Scientific, Germany).

Beyer S., Szewzyk R., Gnirss R., Johne R, & Selinka H.C. (2020). Detection and Characterization of Hepatitis E Virus Genotype 3 in Wastewater and Urban Surface Waters in Germany. Food and Environmental Virology, 12(2), 137-147.

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