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FAQs

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FAQs

Browse our frequently asked technical questions by selecting a product below.

qPCRBIO SyGreen 1-Step Kits FAQs

Beyond what Ct value are results unreliable?

Ct values can vary between template concentrations, reaction optimisation, instruments and laboratories so care must be taken when selecting a cut-off Ct value. Generally, Ct values over 35 would begin to be considered unreliable. However, late Cts could be observed for inefficient reactions using low template copy number. It is always good practice to normalise cut-offs with relative or absolute quantification methods. It is also recommended to run and analyse melt curves or gels of the products to determine products of any late amplifications.

Can I use qPCRBIO SyGreen 1-Step Detect / Go for both one-step and two-step RT-PCR?

No, this kit will not work for 2-step reactions. For 2-step reactions, we recommend the qPCRBIO cDNA Synthesis Kit (PB30.11) or UltraScript 2.0 cDNA Synthesis Kit (PB30.31) for more difficult targets, along with real time PCR kits depending on your needs.

Can the activation time for the hot-start DNA polymerase be altered?

We recommend using a minimum of 2 minutes for activating the polymerase. Longer times of up to 15 minutes can also be used with no detrimental effects to the enzyme.

Do I need 1-step or 2-step reaction?

1-step

Both the cDNA synthesis and PCR reactions occur in the same mix. This option is suited for high throughput applications due to its speed and ease of set up. There is also a reduced risk of contamination. It is not ideal for low quality RNA samples or if the cDNA is required for archive or separate analysis.

2-step

The cDNA synthesis and PCR reactions occur separately. This option is better suited if the cDNA product needs to be retained for analysis. It also allows for higher levels of reaction optimisation. It permits control over the type and concentration of enzyme, RNA input and concentration of cDNA which, in turn, results in higher sensitivity compared to the 1-step format.

Do I need to use an RNase inhibitor in my RT reaction?

No, the RTase Go contains an RNase inhibitor to prevent any degradation and increase sensitivity.

General troubleshooting for low product/late Ct values:

If you are observing unusually late Ct values, try diluting the template RNA. By doing this, you are diluting any inhibitors which may be present to a concentration where they do not inhibit the reaction. Additionally, try increasing the reverse transcription step to 55 °C and increasing the annealing/extension temperatures. This may help resolve difficulties caused by secondary structures present in the RNA template and/or primers.

In cases where reaction inhibition may be involved, try reducing the amount of template1 or add 0.4 – 4.4 mg/ml BSA to the reaction2.

For more specific problems contact technical@pcrbio.com with the following information:

  • Amplicon size
  • Reaction setup
  • Cycling conditions
  • Screen grabs of amplification traces and melting profile

1  Scipioni et al. A SYBR Green RT-PCR assay in single tube to detect human and bovine noroviruses and control for inhibition. Virology Journal.5:94 (2008). doi: 1186/1743-422X-5-94

2  Plante et al. The use of bovine serum albumin to improve the RT‐qPCR detection of foodborne viruses rinsed from vegetable surfaces. Applied Microbiology. 52:3 (2010) doi: https://doi.org/10.1111/j.1472-765X.2010.02989.x

What are the differences between probe and dye-based mixes?

Probe based kits such as qPCRBIO Probe 1-Step Go offer higher sensitivity and are unlikely to show non-template amplifications. Multiplexes can be measured using amplicons with different fluorophores for specific probes, which cannot be achieved using dyes.

Dye based systems such as qPCRBIO SyGreen 1-Step Detect | 1-Step Go detect any intact dsDNA and will therefore show primer dimers and off-target/non-template amplifications. These can be separated from product peaks by analysing melting curves.

What is ROX and do I need it?

ROX is a passive reference dye which means it does not take part in the PCR reaction. It is used to normalise non-PCR related fluctuations in fluorescence. You can use our qPCR Selection Tool under the Resources drop-down menu to determine which of our qPCR mixes are best suited for your qPCR machine.

What is the difference between qPCRBIO SyGreen 1-Step Go and qPCRBIO SyGreen 1-Step Detect?

qPCRBIO SyGreen 1-step Detect has been engineered to have high sensitivity for rapid and accurate results from low template concentrations 1pg of total RNA or 0.01pg of mRNA. qPCRBIO SyGreen 1-step Go has been developed for rapid (early Ct) and accurate results from high template concentrations from 10pg total RNA or 0.01pg of mRNA.

What should I consider if I want to compare qPCRBIO SyGreen 1-Step kit with an alternative manufacturer?

It is important to use what the manufacturer prescribes in the product manual with respect to PCR set up and cycling conditions. It’s also a good idea to use multiple positive controls and to amplify against a template dilution series.

What’s the difference between PCRBIO 1-Step Go RT-PCR Kit, qPCRBIO Probe 1-Step Go and qPCRBIO SyGreen 1-Step Detect|Go Kits?

The PCRBIO 1-step Go RT-PCR Kit has been developed for endpoint RT-PCR. The qPCRBIO Probe 1-Step Go and qPCRBIO SyGreen 1-Step Detect|Go are our probe- and dye-based options for real-time RT-PCR, respectively.

Will this work for micro RNA templates?

Yes, qPCRBIO SyGreen 1-Step Detect | Go can be used for micro RNA templates. Although we do no sell dedicated kits, all of our RTases can be used for miRNA quantification and analysis.

We advise that you use one of the two following approaches:

  • Use universal RT primers and add poly(A) or poly(U) tails (e.g. by poly(U)-polymerase), followed by cDNA synthesis using universal primers1,2.
  • Use specific RT primers and omit the tailing step1,3-5.

If you are unfamiliar with the specifics of those approaches, please refer to the reference list below, which serve as a guideline.

1  Dave, V. P. et al. MicroRNA amplification and detection technologies: opportunities and challenges for point of care diagnostics. Lab Invest 99, 452-469, doi:10.1038/s41374-018-0143-3 (2019).

2  Mei, Q. et al. A facile and specific assay for quantifying microRNA by an optimized RT-qPCR approach. PLoS One 7, e46890, doi:10.1371/journal.pone.0046890 (2012).

3  Chen, C. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33, e179, doi:10.1093/nar/gni178 (2005).

4  Raymond, C. K., Roberts, B. S., Garrett-Engele, P., Lim, L. P. & Johnson, J. M. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 11, 1737-1744, doi:10.1261/rna.2148705 (2005).

5  Androvic, P., Valihrach, L., Elling, J., Sjoback, R. & Kubista, M. Two-tailed RT-qPCR: a novel method for highly accurate miRNA quantification. Nucleic Acids Res 45, e144, doi:10.1093/nar/gkx588 (2017).