Rotor-Gene Multiplex RT-PCR Kit

For ultrafast, multiplex, one-step qRT-PCR gene expression analysis on Rotor-Gene cyclers


  • Optimized for ultrafast, reliable results on Rotor-Gene cyclers
  • Sensitive detection of multiple RNA targets in 1 tube
  • Successful multiplex PCR without the need for optimization
  • Efficient coamplification of low- and high-abundance targets

Product Details

The Rotor-Gene Multiplex RT-PCR Kit is designed for use with the Rotor-Gene Q and other Rotor-Gene cyclers, providing ultrafast, highly reliable quantification in multiplex, real-time one-step RT-PCR using sequence-specific probes. Depending on the cycler configuration, up to 4 RNA targets (e.g., 1 control gene and 3 target genes) can be quantified simultaneously in the same tube. Outstanding performance is achieved through the combination of a specially optimized master mix and the unique Rotor-Gene cycler. For convenience, the master mix can be stored at 2–8°C.


IMPORTANT NOTE: As announced earlier, the production of the Rotor-Gene kits has been discontinued since mid-2021. Hence, these products will be available only until stocks last. Visit the product page of the successor kit to view improved features or to request a trial kit.


For more information and FAQs on this transition, visit:


The Rotor-Gene Multiplex RT-PCR Kit reliably quantifies low- to high-abundance targets in duplex, triplex, and 4-plex assays from as little as 10 pg template, and can detect 10 copies of target (see figures " Reliable duplex analysis" and " Efficient, sensitive duplex analysis"). All targets in a multiplex assay are amplified with equally high PCR efficiency (see figure " Highly efficient 4-plex analysis"). This enables reliable relative quantification, where the expression of a target gene is normalized to that of a control gene.
See figures


Amplifying reference and target genes in the same reaction instead of in separate reactions increases the reliability of gene quantification by minimizing handling errors. The Rotor-Gene Multiplex RT-PCR Kit enables reliable multiplex quantification of RNA targets on the Rotor-Gene Q without the need for optimization of reaction and cycling conditions (see flowchart " QIAGEN multiplex kits"). Real-time one-step RT-PCR is carried out, enabling reverse transcription and PCR to take place sequentially in the same reaction vessel. Since it is not necessary to transfer the finished reverse transcription reaction to another tube for PCR, the real-time RT-PCR procedure is streamlined, making high-throughput analysis possible. 

Highly specific amplification is assured through a balanced combination of K+ and NH4+ ions, which promote specific primer annealing and enable high PCR specificity and sensitivity, while synthetic Factor MP, an innovative PCR additive specially developed for challenging multiplex PCR applications, allows different amplicons in the same reaction to all be amplified with the same high efficiency (see figure "  Unique PCR buffer").

Fast cycling without compromising performance is achieved using Q-Bond, a novel PCR additive that considerably shortens cycler run times (see figure " Fast primer annealing"). In addition, an optimized mix of reverse transcriptases provides efficient cDNA synthesis in just 15 minutes, while the highly stringent hot-start enzyme HotStarTaq Plus DNA Polymerase is rapidly activated at the start of PCR by a brief 5-minute incubation at 95ºC. 

Components of 2x Rotor-Gene Multiplex RT-PCR Kit*
ComponentFeatures Benefits
HotStarTaq Plus DNA Polymerase 5 min activation at 95ºC Set up of qPCR reactions at room temperature
Rotor-Gene Multiplex RT-PCR Buffer Balanced combination of NH4+ and K+ ions Specific primer annealing ensures reliable qPCR results
Synthetic Factor MP Reliable multiplexing analysis of up to 4 genes in the same tube
Unique Q-Bond additive Faster PCR run times enable faster results and more reactions per day
Rotor-Gene RT Mix   Special blend of reverse transcriptases with a high affinity for RNA    RNA can be transcribed in just 15 minutes, even through complex secondary structures
* Also contains dNTP mix (dATP, dCTP, dGTP, dTTP).
See figures


A ready-to-use master mix eliminates the need for optimization of reaction and cycling conditions, such as primer and probe concentrations. Simply add template RNA, primer–probe sets, and the supplied reverse transcriptase mix to the master mix and program the cycler. The handbook supplied with the kit lists recommended dyes and contains a single protocol for all multiplex RT-PCR assays.


The Rotor-Gene Multiplex RT-PCR Kit is optimized for fast, real-time one-step RT-PCR analysis using sequence-specific probes on the Rotor-Gene Q. It is also compatible with the Rotor-Gene 3000 and the Rotor-Gene 6000. Up to 4 RNA targets can be simultaneously and rapidly quantified in the same tube, increasing throughput and saving precious sample material.

Supporting data and figures


ApplicationsReal-time quantification of RNA targets in a multiplex format
Real-time or endpointReal-time
Single or multiplexMultiplex
With or without ROXWithout ROX dye
SYBR Green I or sequence-specific probesSequence-specific probes
Reaction typeReal-time one-step RT-PCR
Sample/target typeRNA
Thermal cyclerRotor-Gene Q, Rotor-Gene 3000, Rotor-Gene 6000


Safety Data Sheets (1)
Download Safety Data Sheets for QIAGEN product components.
Brochures & Guides (1)
Now with even more applications!
Kit Handbooks (1)
For fast multiplex real-time PCR, two-step RT-PCR, and one-step RT-PCR using sequence-specific probes on Rotor-Gene cyclers


Do you have any information or guidelines regarding the choice of reference genes for real-time PCR?

Yes, please visit our website section 'Using endogenous control genes in real-time RT-PCR' for general information. It provides a list of relative gene expression levels for commonly used human and mouse reference genes.

We offer a set of ready-to-order control genes for use in SYBR Green based as well as probe based real-time RT-PCR.

In addition, you may want to refer to the following citations on reference gene selection for quantitative real-time PCR:

• Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, DePaepe A, Speleman F [2002]: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:0034.

• Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A., 2004. Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun. 313(4): 856-62.

• Katrien Smits,Karen Goossens, Ann Van Soom, Jan Govaere, Maarten Hoogewijs, Emilie Vanhaesebrouck,Cesare Galli, Silvia Colleoni, Jo Vandesompele, and Luc Peelman [2009]Selection of reference genes for quantitative real-time PCR in equine in vivo and fresh and frozen-thawed in vitro blastocysts. BMC Res Notes. Dec 11;2:246.

FAQ ID -2371
How important is the RNA purification process, for obtaining reliable qRT-PCR results?

The most important prerequisite for any gene expression analysis experiment is the preparation of consistently high-quality RNA from every experimental sample. Contamination by DNA, protein, polysaccharide, or organic solvents can jeopardize the success of an experiment.

Genomic DNA contamination in an RNA sample compromises the quality of gene expression analysis results. The contaminating DNA inflates the OD reading of the RNA concentration. It is also a source of false positive signals in RT-PCR experiments.

RNase contamination degrades RNA samples whichcauses low signal and false-negative results in PCR.

Residual polysaccharides, collagen, other macromolecules, and organic solvents in an RNA sample can inhibit the activity of DNase, which may interfere with DNase treatment for genomic DNA removal. These contaminants may also inhibit reverse transcriptase and DNA polymerase, leading to lower reverse transcription efficiency and reduced PCR sensitivity.

For fast purification of high-quality RNA we recommend QIAGEN’s RNeasy Kits like the RNeasy Mini Kit, the RNeasy Plus Universal Kit, or the RNeasy FFPE Kit.

FAQ ID -2655
What is the threshold cycle or Ct value?
The Ct or threshold cycle value is the cycle number at which the fluorescence generated within a reaction crosses the fluorescence threshold, a fluorescent signal significantly above the background fluorescence. At the threshold cycle, a detectable amount of amplicon product has been generated during the early exponential phase of the reaction. The threshold cycle is inversely proportional to the original relative expression level of the gene of interest.
FAQ ID -2682
How do you achieve fast cycling, yet still deliver the same performance in PCR as that achieved with standard cycling?

Our unique multiplex PCR buffer system with ammonium and potassium ions and Factor MP has been further optimized in QuantiFast and Rotor-Gene Kits. We have also discovered Q-Bond, a buffer component which supports the rapid formation of the polymerase–primer–template complex, leading to reduced annealing times.

FAQ ID -1430
What is the detection limit of the Rotor-Gene and QuantiFast Multiplex RT-PCR Kits?

The Rotor-Gene and QuantiFast Multiplex RT-PCR Kits allow reliable detection down to 10 target copies. Detection of lower copy numbers down to single copy level may also be possible; however, this depends on the stochastics when working with highly diluted samples. Additional optimization of primer/probe design is usually required.



FAQ ID -2144
Can the Rotor-Gene Multiplex RT-PCR Kit be used on other cyclers?

The specific features of Rotor-Gene Kits and Rotor-Gene cyclers work synergetically to enable an ultrafast-cycling protocol. We do not guarantee that the performance of the Rotor-Gene Multiplex RT-PCR Kit with the same cycling protocol will be the same on other cyclers.



FAQ ID -2142