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  7. Applied Biosystems™ Detection Enhancer, for real-time PCR

Applied Biosystems™ Detection Enhancer, for real-time PCR

Catalog No. A44941
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A44941 500 x 25 μL Reactions
A44811 1000 x 25 μL Reactions
A44810 100 x 25 μL Reactions
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Description

Formulated to improve template amplification in real-time PCR (qPCR) workflows

  • Detection Enhancer is uniquely formulated to improve template amplification in real-time PCR (qPCR) workflows. This reagent is particularly beneficial with DNA samples containing GC-rich sequences and/or persistent secondary structure. Detection Enhancer is a component of the AgPath-ID One-Step RT-qPCR Reagents kit and is offered here as a stand-alone product that can be used with any Applied Biosystem real-time PCR master mix.
  • Improve qPCR amplification of templates containing high GC content and persistent secondary structure
  • Compatible with any Applied Biosystem real-time PCR master mix
  • Flexible kit sizes for a range of laboratory throughputs
  • GC-rich DNA sequences are usually defined as those that contain >60% cytosine (C) or guanine (G). GC-rich samples can be particularly challenging to amplify because the sequences are more stable than those with lower GC content. In qPCR experiments, this results in a higher DNA melting point. In addition, GC-rich sequences can form secondary structure, which can add further amplification challenges. Adding a small volume of Detection Enhancer to your reaction mix can dramatically improve qPCR amplification in GC-rich samples.
  • Detection Enhancer is specifically formulated to address qPCR amplification in particularly stable DNA sequences. It is only for use in real-time PCR workflows where amplification is affected by templates that are GC rich and/or contain persistent secondary structure. The reagents may affect sensitivity for other target types, so it is recommended to first assemble the reaction without Detection Enhancer. If no signal is observed from samples that are expected to be positive, then add Detection Enhancer to the reaction.
  • The recommended volume of Detection Enhancer per 25 μL reaction is 1.67 μL. For more information on applications of Detection Enhancer, please see the AgPath-ID One-Step RT-qPCR Reagents kit user guide

Specifications

Content And Storage 1 x 1.2 mL Detection Enhancer, store at -5 to -30°C
Detection Method Primer-probe
GC-Rich PCR Performance High
PCR Method 1-step RT-qPCR
Reaction Speed Standard
For Use With (Equipment) 7500 System
Product Line Applied Biosystems
Product Type Detection Enhancer
Quantity 500 reactions
Shipping Condition Dry Ice
For Use With (Application) Real Time PCR (qPCR)
No. of Reactions 500 x 25 μL Reactions
Sample Type Viral Samples
Volume 1.2 mL
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Frequently Asked Questions (FAQs)

With the AgPath-ID One-Step RT-PCR Reagents, I am getting signal detection in the no-template control (NTC) reaction. Why is this?

This is likely due to PCR contamination. Here are some recommendations:

- Repeat the qRT-PCR reaction with fresh reagents and decontaminated pipettors.
- Set up and run the qRT-PCR reaction in an area that is isolated from areas used for nucleic acid isolation and PCR product analysis.
- The Reverse Transcriptase enzyme contained in this kit is produced using an E. coli expression vector containing a proprietary version of the MMLV pol gene (GenBank accession no. J02255) expressed from pET-24(+). It is possible that a minimal amount of the expression vector could be carried over into the final mastermix formulation. If you are targeting MMLV, a related virus, or any of the plasmid sequence, we recommend designing primer sequences for target sequences not contained in the expression vector.
What can I do to improve the sensitivity of my qPCR assay?

If you are targeting a low-abundance gene, you may have trouble getting Ct values in a good, reliable range (Ct > 32). To increase the sensitivity of the assay, you may want to consider the following:

- Increase the amount of RNA input into your reverse transcription reaction, if possible
- Increase the amount of cDNA in your qPCR reaction (20% by volume max)
- Try a different reverse transcription kit, such as our SuperScript VILO Master Mix, for the highest cDNA yield possible
- Consider trying a one-step or Cells-to-CT type workflow (depending on your sample type)

How do I set the baseline for my qPCR experiment?

Most times your instrument software can automatically set a proper baseline for your data. Check out our short video, Understanding Baselines, for more information on how to set them (https://www.youtube.com/watch?feature=player_embedded&v=5BjFAJHW-bE).

How do I set the threshold for my qPCR experiment?

In most cases your instrument software can automatically set a proper threshold for your data. Check out our short video, Understanding Thresholds, for more information on how to set them (https://www.youtube.com/watch?feature=player_embedded&v=H_xsuRQIM9M).

I am not getting any amplification with my TaqMan Assay or SYBR Green primer set. What is causing this?

There could be several reasons for no amplification from an assay or primer set. Please see these examples and suggested solutions in our Real-Time Troubleshooting Tool (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/real-time-pcr-troubleshooting-tool/gene-expression-quantitation-troubleshooting/no-amplification.html) for more details.

I am getting amplification in my no-template control (NTC) wells in my qPCR experiment. What is causing this?

There could be several reasons for amplification in a NTC well. Please see these examples and suggested solutions in our Real-Time Troubleshooting Tool (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/real-time-pcr-troubleshooting-tool/gene-expression-quantitation-troubleshooting/amplification-no-template-control.html) for more details.

My amplification curves have a funny shape in my qPCR experiment. What is causing this?

There are several reasons that amplification could be delayed. Please see the information in our Real-Time Troubleshooting Tool (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/real-time-pcr-troubleshooting-tool/gene-expression-quantitation-troubleshooting/abnormal-amplification-curves/amplification-occurs-later.html) for more details.

What can I do if the amplification of my target gene is later than expected for my qPCR experiment?

There are several reasons that amplification could be delayed. Please see the information in our Real-Time Troubleshooting Tool for more details (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/real-time-pcr-troubleshooting-tool/gene-expression-quantitation-troubleshooting/abnormal-amplification-curves/amplification-occurs-later.html).

Can I use my SYBR Green primers for a TaqMan assay?

It may be possible to use your SYBR Green primers for a TaqMan assay, depending on how they were designed. You would have to design a separate probe to use with your existing primers. Please refer to the guidelines in this manual (https://tools.thermofisher.com/content/sfs/manuals/cms_041902.pdf) on “Manually Designing Primers and Probes” for the next steps. If you have Primer Express Software, you can use that software to design a probe. Please note that restricting the design using the predesigned SYBR primers may not allow for a successful probe design.

Do I have to normalize my samples for comparative Ct experiments?

Comparative Ct experiments use an endogenous control gene to normalize the cDNA input. Please watch this short video (https://www.youtube.com/watch?feature=player_embedded&v=jst-3hD_xFQ) for more details on how this works. For a protocol workflow, please refer to our Guide to Performing Relative Quantitation of Gene Expression (https://tools.thermofisher.com/content/sfs/manuals/cms_042380.pdf).

What are the requirements for a relative quantification qPCR experiment?

In a relative quantification experiment, you will need to identify an endogenous control and a reference (or calibrator) sample. An endogenous control is a gene that does not change in expression across all the samples in your study. A reference sample is the sample that you are comparing all others to. This is often the untreated, or control, sample. Please see our Relative Gene Expression Workflow bulletin (https://tools.thermofisher.com/content/sfs/brochures/cms_075428.pdf) for more step-by-step guidelines on how to design your experiment.

What are the requirements for a standard curve qPCR experiment?

In a standard curve experiment, you must generate a standard curve for each target gene. The standards should closely represent the sample (i.e., RNA for RNA input, plasmid or gDNA for DNA input). This reference (http://www.ncbi.nlm.nih.gov/pubmed/11013345) is a good review of standard curves and the experimental setup. You can also review this short video (https://www.youtube.com/watch?v=mE5ieko9_RQ) on standard curve experiments.

What is the difference between absolute quantification (AQ) and relative quantification (RQ)? How do I choose which method to use?

Absolute quantification will quantitate unknowns based on a known quantity. It involves the creation of a standard curve from a target of known quantity (i.e., copy number). Unknowns can then be compared to the standard curve and a value can be extrapolated. Absolute quantification is useful for quantitating copy number of a certain target in DNA or RNA samples. The result usually is a number followed by a unit, such as copy number and ng, etc.

Relative quantification can quantitate a fold difference between samples. It involves the comparison of one sample to another sample (calibrator) of significance. For example, in a drug treatment study you could compare a treated to an untreated sample. The quantity of the calibrator is not known and cannot be measured absolutely. Therefore the calibrator (untreated sample) and samples (treated samples) are normalized to an endogenous control (a gene that is consistently expressed among the samples) and then compared to each other to get a fold difference. Relative quantification is useful for quantitating messenger RNA levels. Since the result is a fold change or ratio, it is not followed by a unit.

The method that you choose will depend on the type of data you need from your experiment. You can find more information here (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html) as well.

Can I do a melt curve with a TaqMan assay?

No. A TaqMan probe, once cleaved, cannot be re-quenched. Therefore a melt curve does not apply when using a TaqMan assay.

What is the difference between TaqMan and SYBR Green methods of detection?

TaqMan and SYBR Green chemistries are two different methods of detection for qPCR. Please see this detailed comparison of these two approaches (https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/qpcr-education/taqman-assays-vs-sybr-green-dye-for-qpcr.html). You can also watch this short video (https://www.youtube.com/watch?feature=player_embedded&v=fkUDu042xic) on how TaqMan assays work.

How many replicates do I need to run for my qPCR experiment? What recommendations do you have for plate setup?

Please view this short video (https://www.youtube.com/watch?v=eIaPGhOjBQo), which explains some best practices for replicates and plate setup.

What are the different phases of a qPCR reaction?

Check out this short video (https://www.youtube.com/watch?feature=player_embedded&v=4sXPUbIrh3A) to understand the different phases of the PCR reaction and why they are important.

I'm trying to decide between purchasing a one-step or two-step RT-PCR kit. Can you review the advantages and disadvantages of each?

One-step RT-PCR is convenient and less prone to contamination, as there is less opportunity for pipetting error. This method is also faster than the two-step process. However, the cDNA cannot be archived, and fewer genes can be analyzed. Two-step RT-PCR gives you the ability to archive cDNA, analyze multiple genes, and offers greater flexibility. Learn more about the difference between one-step and two-step RT-PCR on this page Onestep vs Twostep RT-PCR.
Is the Detection Enhancer, for real-time PCR still included with the AgPath ID One-Step RT-PCR Reagents?

No, in an effort to improve the impact on environmental health and comply with chemical safety labeling, the Detection Enhancer component was removed from the AgPath ID One-Step RT-PCR Reagents. It is now available for purchase separately. Here are the part numbers for the stand-alone Detection Enhancer, for real-time PCR:
Cat. No. A44810: Detection Enhancer, 100 reactions
Cat. No. A44941: Detection Enhancer, 500 reactions
Cat. No. A44811: Detection Enhancer, 1000 reactions

For Research Use Only. Not for use in diagnostic procedures.