Rotor-Gene SYBR® Green PCR Kit
For ultrafast, real-time PCR and two step RT-PCR using SYBR Green on Rotor-Gene cyclers
For ultrafast, real-time PCR and two step RT-PCR using SYBR Green on Rotor-Gene cyclers
The Rotor-Gene SYBR Green PCR Kit is designed for use with the Rotor-Gene Q and other Rotor-Gene cyclers, providing ultrafast, highly specific quantification of gDNA and cDNA targets with quantitative real-time PCR or two-step RT-PCR using SYBR Green I detection. Outstanding qPCR 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: www.qiagen.com/PCRresource.
The Rotor-Gene SYBR Green PCR Kit is well suited for use in gene expression analysis of cDNA targets (see figures " Highly specific and sensitive detection" and " Reliable and specific detection down to 10 copies").
When QuantiTect Primer Assays are used together with the Rotor-Gene SYBR Green PCR Kit, highly sensitive quantification of specific PCR products is achieved without the need for optimization (see table).
|CT||Mean deviation||CT||Mean deviation|
|BAX (BCL2-associated X protein)||24.84||0.05||29.57||0.46|
|BCL2 (apoptosis gene)||26.96||0.05||32.83||0.29|
|b-Actin (housekeeping gene)||20.24||0.03||24.39||0.12|
The Rotor-Gene SYBR Green PCR Kit enables rapid and reliable real-time PCR quantification on the Rotor-Gene Q without the need for optimization of reaction and cycling conditions. The fluorescent dye SYBR Green I in the master mix enables the analysis of many different targets without having to synthesize target-specific labeled probes. Highly specific amplification is assured through a balanced combination of K+ and NH4+ ions, which promote specific primer annealing, enabling high PCR specificity and sensitivity (see figure " Specific primer annealing"). Fast cycling without compromising performance is achieved using Q-Bond, a novel PCR additive that enables cycler run times of as low as 45 minutes (see figure " Fast primer annealing").
|HotStarTaq Plus DNA Polymerase||5 min activation at 95ºC||Set up of qPCR reactions at room temperature|
|Rotor-Gene SYBR Green PCR Buffer||Balanced combination of NH4+ and K+ ions||Specific primer annealing ensures reliable qPCR results|
|Unique Q-Bond additive||Faster PCR run times enable faster results and more reactions per day|
|SYBR Green I dye||Yields a strong fluorescent signal upon binding double-stranded DNA||Highly sensitive quantification|
The Rotor-Gene SYBR Green PCR Master Mix eliminates the need for optimization of reaction and cycling conditions. Simply add DNA template DNA and primers to the master mix and program the cycler. Instructions are provided in the detailed handbook supplied with the kit.
For gene expression analysis using real-time two-step RT-PCR, the combination of the Rotor-Gene SYBR Green PCR Kit, QuantiTect Reverse Transcription Kit, QuantiTect Primer Assays, and Rotor-Gene Q provides a complete, ready-to-run solution. The QuantiTect Reverse Transcription Kit delivers fast cDNA synthesis in just 20 minutes with integrated removal of genomic DNA contamination. QuantiTect Primer Assays are bioinformatically validated primer sets for any gene from human, mouse, rat, and many other species. Assays can be easily ordered online at the GeneGlobe Web portal.
The Rotor-Gene SYBR Green PCR Kit provides rapid real-time quantification of cDNA and gDNA targets on the Rotor-Gene Q. The Kits are also compatible with the Rotor-Gene 3000 and the Rotor-Gene 6000.
For ultrafast, one-step qRT-PCR gene expression analysis of RNA targets using SYBR Green I on Rotor-Gene cyclers, use the Rotor-Gene SYBR Green RT-PCR Kit.
|Applications||Real-Time quantification of genomic DNA or cDNA targets|
|Thermal cycler||Rotor-Gene Q, Rotor-Gene 3000, Rotor-Gene 6000|
|Reaction type||Real-time PCR and two-step RT-PCR|
|SYBR Green I or sequence-specific probes||SYBR Green I|
|Description||For ultrafast quantitative real-time PCR and two-step RT-PCR using SYBR Green I on Rotor-Gene cyclers|
|Single or multiplex||Single|
|Real-time or endpoint||Real-time|
|With or without ROX||Without ROX dye|
|Sample/target type||DNA, cDNA|
Yes, please follow the Supplementary Protocols at the links below:
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 : 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 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.
Any DNA contamination will artificially inflate the SYBR Green signal, yielding skewed gene expression profiles and false-positive signals. The most common source of DNA contamination is from PCR products generated during previous experiments. Such contamination is most often due to the improper disposal of tubes, tips, and gels that previously came into contact with PCR products. Additionally, PCR products may also contaminate pipettors, racks, work pads, and commonly used reagents such as water and buffers. To minimize the risk of contaminating your experiment with extraneous DNA, the following steps should be taken:
QuantiTect Primer Assays are primer pairs designed and bioinformatically validated specifically for real-time RT-PCR with SYBR Green detection. To find a primer assay for your target gene of interest, please visit our GeneGlobe data base.
For best results, we strongly recommend using QuantiTect Primer Assays in combination with QIAGEN's products for SYBR Green-based Real-Time PCR and RT-PCR.
This type of cycling allows a significant reduction in cycling time for Rotor-Gene SYBR Green PCR Kits. It is more effective than reducing the individual times for annealing and extension.
The buffer composition, which affects the initial reactivation of HotStarTaq Plus DNA Polymerase, has been optimized for each respective Rotor-Gene Kit.
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.
Assuming 100% amplification efficiency, each step increase in Ct value represents a doubling in the amount of qPCR template. Therefore, evaluating the difference in Ct values between the qPCR assay, and its matching NRT control, leads to the following predictions:
|CtNRT - Ct+RT||Fraction of gene expression signal due to contaminating DNA||Percentage of gene expression signal due to contaminating DNA|
|1||(1/21) = 1/2||50%|
|2||(1/22) = 1/4||25%|
|3||(1/23) = 1/8||13%|
|4||(1/24) = 1/16||6%|
|5||(1/25) = 1/32||3%|
Dissociation curves are carried out at the end of a PCR experiment by following a 3-step procedure.
First, all the components are denatured at 95°C, followed by complete annealing at a set temperature (based on the primer Tm values), followed by a gradual increase in temperature up to 95°C. Fluorescence intensity is monitored during this final temperature increase, resulting in the generation of a melting curve or dissociation curve.
By analyzing the first derivative of such a curve, you can readily assess the homogeneity of the PCR products, including the presence of primer–dimers, thereby determining the specificity of the PCR reaction. It is important to carry out such post-PCR analyses when using SYBR Green probe chemistry due to this reagent's lack of sequence specificity.
We have performed numerous tests comparing the performance of Rotor-Gene SYBR Green PCR Kits and QuantiTect Kits with QuantiTect Primer Assays. Due to the optimized ion concentrations in the PCR buffers, both perform equally well with QuantiTect Primer Assays and do not require any adjustment of primer concentration.
Rotor-Gene Kits are specifically developed for the Rotor-Gene Q PCR Cycler. The unique rotary system of the cycler combined with the kits’ proprietary buffer system enable ultrafast cycling. Rotor-Gene Kits do not contain ROX dye since no normalization to a passive reference is required. Also, Rotor-Gene Kits do not contain dUTP; therefore, UNG pretreatment is not possible.
If the extra peaks seem irregular or noisy, do not occur in all samples, and occur at temperatures less than 70 ºC, then these peaks may not represent real PCR products and instead may represent artifacts caused by instrument settings.
Usually extra peaks caused by secondary products are smooth and regular, occur reproducibly in most samples, and occur at temperatures greater than 70 ºC. Characterization of the product by agarose gel electrophoresis is the best way to distinguish between these cases. If only one band appears by agarose gel then the extra peaks in the dissociation curve are instrument artifacts and not real products. If this is the case, refer to the thermal cycler user manual, and confirm that all instrument settings (smooth factor, etc.) are set to their optimal values.