QuantiTect PCR Kits

Pour qPCR et qRT-PCR en deux étapes avec SYBR Green I et qPCR et qRT-PCR en deux étapes ainsi que qPCR multiplex et qRT-PCR multiplex deux étapes avec sondes spécifiques de la séquence

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QuantiTect Probe PCR Kit (200)

Cat. No. / ID: 204343

Pour 200 x 50 µl de réactions : 3 x 1,7 ml 2x de QuantiTect Probe PCR Master Mix, 2 x 2 ml de RNase-Free Water

Kit

QuantiTect PCR Kit

QuantiTect PCR +UNG Kit

Detection type

Probe

Multiplex Probe

SYBR Green

Reactions

200

1000

Inquire

Les QuantiTect PCR Kits sont destinés aux applications de biologie moléculaire. Ces produits ne sont pas conçus pour le diagnostic, la prévention ou le traitement des maladies.

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Caractéristiques

Détection très sensible de cibles à faible nombre de copies
qPCR à l’aide de sondes spécifiques de la séquence ou de SYBR Green
Quantification précise sur plusieurs logs de matrice
Pas besoin d’optimiser les conditions de réaction et de thermocyclage
Détection d’un maximum de 5 cibles dans le même tube

Détails produit

Les QuantiTect PCR Kits (qPCR kits) permettent une quantification sensible des cibles ADNg et ADNc par PCR en temps réel et RT-PCR en deux étapes à l’aide de sondes spécifiques de la séquence ou la détection SYBR Green I. Les kits de real-time PCR permettent également de quantifier de manière fiable jusqu’à 5 cibles d’ADNg ou d’ADNc dans un seul tube par real-time PCR ou RT-PCR multiplex en deux étapes. La combinaison d’un hot start et d’un système de tampon PCR unique dans le mélange principal prêt à l’emploi garantit une qPCR très sensible sur n’importe quel thermocycleur en temps réel, sans besoin d’optimisation. Le mélange de dNTP comprend du dUTP ce qui permet un traitement optionnel à l’UNG. Pour des raisons de commodité, les mélanges maîtres des QuantiTect PCR Kits peuvent être conservés entre 2 et 8 °C.

Deux formats de kits sont disponibles pour la PCR multiplex utilisant des sondes spécifiques à une séquence : le QuantiTect Multiplex PCR kit pour les thermocycleurs qui nécessitent le colorant ROX pour la normalisation de la fluorescence, et le QuantiTect Multiplex PCR NoROX kit pour tous les autres thermocycleurs.

Performances

La HotStarTaq DNA Polymerase incluse dans les kits de PCR quantitative QuantiTect augmente la spécificité de la réaction PCR en fournissant le hot start le plus strict par rapport aux autres polymérases.

Les QuantiTect SYBR Green PCR Kits permettent une quantification spécifique sur une large plage linéaire (voir figure « Quantification spécifique sur une large plage linéaire »). Les QuantiTect SYBR Green PCR Kits fournissent des résultats sensibles et fiables lorsqu’ils sont utilisés en combinaison avec le QuantiTect Reverse Transcription Kit et les QuantiTect Primer Assays (voir figure « Quantification spécifique et sensible »).

Les QuantiTect Probe PCR Kits fournissent des résultats sensibles et fiables en combinaison avec le QuantiTect Reverse Transcription Kit (voir figure « Une sensibilité et une efficacité élevées, ainsi qu’une large plage dynamique »). La composition unique du tampon PCR permet aux QuantiTect Probe PCR Kits de fournir une quantification sensible des cibles d’ADN à faible taux de copie, ainsi qu’une quantification précise sur une large plage linéaire (voir la figure « Large plage dynamique dans la real-time PCR »).

Le QuantiTect Multiplex PCR Master Mix garantit que les produits PCR dans une réaction multiplex sont amplifiés avec la même efficacité et la même sensibilité que les produits PCR dans les réactions d’amplification simple correspondantes (voir le tableau « Valeurs de cycle seuil [C_Τ] comparables avec les PCR triplex et singleplex », et la figure « Résultats comparables avec les PCR 4-plex et singleplex »).

Valeurs de cycle seuil (CT) comparables avec les PCR triplex et singleplex
	Détection d’une séquence de translocation t(8;14) (20 copies)	Détection d’une séquence d’ADNc de la GAPDH (10⁶ copies)	Détection d’une séquence d’ADNc du NFKB (voir première colonne pour le nombre de copies)
PCR triplex avec 10⁵ copies de NFKB	34,31	20,37	21,92
PCR singleplex correspondantes	34,07	20,54	21,83
PCR triplex avec 10⁴ copies de NFKB	34,61	20,62	25,03
PCR singleplex correspondantes	34,00	20,46	25,19
PCR triplex avec 10³ copies de NFKB	35,17	19,94	28,38
PCR singleplex correspondantes	34,43	20,50	28,65

Les kits permettent de détecter jusqu’à 10 copies d’un gène cible, même si le nombre de copies du gène de référence dans la même réaction est jusqu’à 10⁶ fois supérieur (voir la figure « Détection de 10 copies du gène cible avec un excès de gène de référence. » et le tableau correspondant « Succès de la qPCR quantitative triplex de cibles peu abondantes et très abondantes »).

Succès de la real-time PCR quantitative triplex de cibles peu abondantes et très abondantes
Mélange de matrices 1	1 400 copies	10⁶ copies	2 x 10⁴ copies
	Détection de la CSBG	Détection de la GAPDH	Détection de la HSP
Valeurs C_T pour la PCR triplex	27,73	18,69	23,59
Valeurs C_T pour les PCR singleplex	27,08	18,89	23,52
Mélange de matrices 2	140 copies	10⁶ copies	2 x 10³ copies
Valeurs C_T pour la PCR triplex	31,11	19,00	27,05
Valeurs C_T pour les PCR singleplex	30,66	18,61	26,97
Mélange de matrices 3	14 copies	10⁶ copies	2 x 10² copies
Valeurs C_T pour la PCR triplex	34,74	18,98	30,71
Valeurs C_T pour les PCR singleplex	33,84	19,01	30,38

Voir les illustrations

Quantification spécifique sur une large plage linéaire.

Quantification spécifique et sensible.

Une sensibilité et une efficacité élevées, ainsi qu’une large plage dynamique.

Large plage dynamique dans la real-time PCR.

Résultats comparables entre la PCR 4-plex et les PCR singleplex correspondantes.

Détection de 10 copies du gène cible avec un excès de gène de référence.

Principe

Les QuantiTect SYBR Green PCR Kits contiennent un mélange principal optimisé et prêt à l’emploi pour la quantification en temps réel hautement spécifique et sensible des cibles ADNc à l’aide du SYBR Green I (voir tableau « Composants de 2x QuantiTect SYBR Green PCR Kit »). Le fluorescent dye SYBR Green I contenu dans le master mix permet d’analyser de nombreuses cibles différentes sans avoir à synthétiser des sondes marquées spécifiques à la cible. Une combinaison équilibrée d’ions K⁺ et NH₄⁺ dans le tampon PCR favorise une renaturation spécifique des amorces et permet une spécificité et une sensibilité élevées de la PCR (voir figure « Renaturation spécifique des amorces »). De plus, la HotStarTaq DNA Polymerase assure un hot start rigoureux, empêchant la formation de produits non spécifiques.

Composants du 2x QuantiTect SYBR Green PCR Kit
Composant	Caractéristiques	Avantages
HotStarTaq DNA Polymerase	15 min d’activation à 95 ºC	Réglage des réactions qPCR à température ambiante
QuantiTect SYBR Green PCR Buffer	Combinaison équilibrée d’ions NH₄⁺ et K⁺	La renaturation spécifique des amorces garantit des résultats fiables de la PCR
Mélange dNTP	Comprend du dUTP, qui remplace partiellement le dTTP et permet un traitement UNG optionnel des réactions	Élimine la contamination de transfert des produits PCR grâce au traitement UNG optionnel
Colorant SYBR Green I	Produit un signal fluorescent puissant lors de la liaison de l’ADN double brin	Quantification très sensible
Colorant ROX	Pour la normalisation des signaux fluorescents sur les appareils Applied Biosystems et, en option, Agilent	Quantification précise sur les thermocycleurs qui nécessitent le colorant ROX. N’interfère pas avec les réactions sur d’autres thermocycleurs en temps réel

Les QuantiTect Probe PCR Kits contiennent un mélange principal optimisé et prêt à l’emploi pour la quantification en temps réel hautement spécifique et sensible des cibles ADNg et ADNc à l’aide de sondes spécifiques de la séquence (voir tableau « Composants de 2x QuantiTect Probe PCR Kit »). Les kits sont conçus pour être utilisés avec tous les types de sondes spécifiques à une séquence, y compris la détection des sondes d’hydrolyse (par exemple, TaqMan® et autres sondes à double marquage), les sondes FRET et les balises moléculaires. Les QuantiTect Probe PCR Kits contiennent un tampon PCR unique qui renferme une combinaison équilibrée d’ions K⁺ et NH₄⁺. Ces derniers favorisent la renaturation spécifique des amorces, ce qui permet une spécificité et une sensibilité élevées de la PCR (voir la figure « Renaturation spécifique des amorces »). De plus, la HotStarTaq DNA Polymerase assure un hot start rigoureux, empêchant la formation de produits non spécifiques.

Composants de 2x QuantiTect Probe PCR Kit
Composant	Caractéristiques	Avantages
HotStarTaq DNA Polymerase	15 min d’activation à 95 ºC	Réglage des réactions qPCR à température ambiante
QuantiTect Probe PCR Buffer	Combinaison équilibrée d’ions NH₄⁺ et K⁺	La renaturation spécifique des amorces garantit des résultats fiables de la PCR
Mélange dNTP	Comprend du dUTP, qui remplace partiellement le dTTP et permet un traitement UNG optionnel des réactions	Élimine la contamination de transfert des produits PCR grâce au traitement UNG optionnel
Colorant ROX	Pour la normalisation des signaux fluorescents sur les appareils Applied Biosystems et, en option, Agilent	Quantification précise sur les thermocycleurs qui nécessitent le colorant ROX. N’interfère pas avec les réactions sur d’autres thermocycleurs en temps réel

Les QuantiTect Multiplex PCR Kits permettent de réussir une RT-PCR multiplex en deux étapes dès la première tentative (voir l’organigramme « Kits multiplex QIAGEN »). Le mélange principal optimisé garantit que les produits PCR dans une réaction multiplex sont amplifiés avec la même efficacité et la même sensibilité que les produits PCR dans des réactions d’amplification simples correspondantes. Le kit permet de détecter jusqu’à 10 copies d’un gène cible.

L’amplification des gènes de référence et des gènes cibles dans la même réaction plutôt que dans des réactions séparées augmente la fiabilité de la quantification des gènes en minimisant les erreurs de manipulation. LeQuantiTect Multiplex PCR Master Mix contient une combinaison équilibrée d’ions K⁺ et NH₄⁺ ainsi que le Factor MP synthétique unique qui, ensemble, favorisent une renaturation stable et efficace des amorces et des sondes à la matrice d’acide nucléique, ce qui permet une grande efficacité de la PCR (voir le tableau « Composants du 2x QuantiTect Multiplex PCR Kit »). De plus, la HotStarTaq DNA Polymerase assure un hot start rigoureux, empêchant la formation de produits non spécifiques.

Les mélanges principaux des QuantiTect PCR Kits contiennent également du dUTP, ce qui permet un prétraitement avec l’uracil-N-glycosylase (UNG) avant de commencer la PCR, ce qui garantit que tout produit PCR contaminant n’affecte pas les réactions PCR ultérieures.

Composants du 2x QuantiTect Multiplex PCR Kit
Composant	Caractéristiques	Avantages
HotStarTaq DNA Polymerase	15 min d’activation à 95 ºC	Réglage des réactions qPCR à température ambiante
QuantiTect Multiplex PCR Buffer	Combinaison équilibrée d’ions NH₄⁺ et K⁺	La renaturation spécifique des amorces garantit des résultats fiables de la PCR
QuantiTect Multiplex PCR Buffer	Synthetic Factor MP	Analyse multiplexe fiable d’un maximum de 4 gènes dans le même tube
Mélange dNTP	Comprend du dUTP, qui remplace partiellement le dTTP et permet un traitement UNG optionnel des réactions	Élimine la contamination de transfert des produits PCR grâce au traitement UNG optionnel
Colorant ROX*	Normalise les signaux fluorescents sur les appareils Applied Biosystems et, en option, Agilent	Quantification précise sur les thermocycleurs qui nécessitent le colorant ROX. N’interfère pas avec les réactions sur d’autres thermocycleurs en temps réel

Voir les illustrations

Réussite de l’analyse génotypique multiplex basée sur la PCR.

Procédure

Si nécessaire, il est possible de prétraiter les réactions avec de l’uracile-N-glycosylase (UNG) afin d’éliminer le transfert des produits de PCR des réactions précédentes. Pour des résultats optimaux lors de la RT-PCR en temps réel en deux étapes, nous recommandons de synthétiser l’ADNc à l’aide du QuantiTect Reverse Transcription Kit. Le kit permet une synthèse rapide de l’ADNc en seulement 20 minutes avec élimination intégrée de la contamination par l’ADN génomique.

Le QuantiTect SYBR Green et lS Probe PCR Kits permettent de s’affranchir de l’optimisation des conditions de réaction, qui peut s’avérer fastidieuse et chronophage. Il suffit d’ajouter les amorces et la matrice d’ADN au mélange principal PCR prêt à l’emploi et de lancer la réaction. Suivez le protocole du manuel pour obtenir des résultats rapides et fiables sur n’importe quel thermocycleur en temps réel.

La combinaison des QuantiTect SYBR Green PCR Kits et des QuantiTect Primer Assays garantit des résultats hautement spécifiques dans l’analyse de l’expression des gènes. Il s’agit d’ensembles d’amorces validés sur le plan bioinformatique et couvrant l’ensemble du génome, qui permettent de détecter des transcriptions chez l’homme, la souris, le rat et de nombreuses autres espèces. Vous pouvez facilement commander les dosages d’amorces QuantiTect en ligne sur le site de GeneGlobe.

Les QuantiTect Multiplex PCR Kits contiennent des mélanges maîtres prêts à l’emploi qui éliminent le besoin d’optimiser les conditions de réaction et de thermocyclage. Le manuel contient un protocole unique que vous pouvez utiliser avec tous les thermocycleurs disponibles, ainsi qu’une liste des colorants recommandés.

Les kits sont disponibles avec ou sans colorant de référence passif ROX dans le mélange principal, ce qui permet de les utiliser sur pratiquement tous les thermocycleurs en temps réel (voir le tableau « Choix du QuantiTect Multiplex PCR Kit approprié »). L’analyse automatique des données permet de détecter même les faibles nombres de copies grâce aux concentrations optimisées de ROX.

Choix du QuantiTect Multiplex PCR Kit approprié
Colorant ROX	Kit	Thermocycleurs compatibles
Fourni dans le mélange principal	QuantiTect Multiplex PCR Kit	Thermocycleurs d’Applied Biosystems
Absent du mélange principal	QuantiTect Multiplex PCR NoROX Kit	Rotor-Gene cyclers, et thermocycleurs de Bio-Rad, Cepheid, Eppendorf, Roche, Agilent, et d’autres fournisseurs

Applications

Les QuantiTect PCR Kits permettent l’analyse de l’expression génétique de l’ADNc ou la quantification de l’ADNg sur n’importe quel thermocycleur en temps réel. Il s’agit notamment des appareils d’Applied Biosystems, de Bio-Rad, de Cepheid, d’Eppendorf, de Roche et d’Agilent. Pour le Rotor‑Gene Q et les autres thermocycleurs Rotor-Gene, nous recommandons d’utiliser le Rotor-Gene SYBR Green PCR Kit, le Rotor-Gene Probe PCR Kit ou le Rotor-Gene Multiplex PCR Kit, qui ont été spécialement développés pour le thermocyclage rapide sur ces appareils.

Comparaison des QuantiTect PCR Kits
Caractéristiques	QuantiTect SYBR Green PCR Kits	QuantiTect Probe PCR Kits	QuantiTect Multiplex PCR Kits
Applications	Quantification en temps réel des cibles d’ADN génomique ou d’ADNc	Quantification en temps réel des cibles d’ADN génomique ou d’ADNc	Quantification en temps réel des cibles d’ADN génomique ou d’ADNc
Type de réaction	PCR et RT-PCR en deux étapes	PCR et RT-PCR en deux étapes	PCR multiplex et RT-PCR multiplex en deux étapes
Temps réel ou point final	Temps réel	Temps réel	Temps réel
Type d’échantillon/de cible	ADN, ADNc	ADN, ADNc	ADN, ADNc
Simple ou multiplex	Unique	Unique	Multiplex
SYBR Green I ou sondes à une séquence spécifique	SYBR Green I	Sondes spécifiques à une séquence	Sondes spécifiques à une séquence
Thermocycleur	Tous les thermocycleurs en temps réel (par exemple, LightCycler, Rotor-Gene, ABI)	La plupart des thermocycleurs en temps réel (par exemple, LightCycler, Rotor-Gene, ABI)	La plupart des thermocycleurs en temps réel (par exemple, LightCycler, Rotor-Gene, ABI)
Avec ou sans ROX	Avec ROX	Avec ROX	Avec ou sans ROX

Données et illustrations utiles

Quantification spécifique sur une large plage linéaire.

Des dilutions d’ADNc de leucocytes humains ont été analysées sur le Rotor‑Gene 3000 à l’aide du dosage QuantiTect Primer Assay pour le gène humain BAX et des kits indiqués. La quantification hautement spécifique avec le kit et le dosage QuantiTect est démontrée par le pic unique dans l’analyse de la courbe de fusion et la courbe plate pour la réaction NTC. NTC : Contrôle sans matrice. Fluo. norm. : Fluorescence normalisée.

Ressources

For use with QuantiTect PCR Kits to eliminate carryover of PCR products

For genomewide, ready-to-use real-time RT-PCR assays using SYBR Green detection

QuantiTect Multiplex PCR Kit - with master mix containing ROX passive reference dye QuantiTect Multiplex PCR NoROX Kit - with master mix free of ROX passive reference dye For quantitative, multiplex, real-time PCR and two-step RT-PCR using sequence-specific probes

For quantitative, real-time PCR and two-step RT-PCR using sequence-specific probes

For quantitative, real-time PCR and two-step RT-PCR using SYBR Green I

FAQ

QuantiTect SYBR Green PCR Kits contain buffers with different salt concentrations compared to Roche Kits, resulting in different template melting temperatures. We recommend to decrease the annealing temperature by at least by 5°C when using a QuaniTect SYBR Green PCR Kit.

FAQ ID -1083

So far, we have seen excellent stability of UNG in QuantiTect PCR Master Mixes. Therefore, UNG can be added to a fresh tube of master mix and be stored as recommended for the master mix in the respective handbook.

FAQ ID -2138

Ensure PCR amplicons are as short as possible, ideally 60–150 bp. Always use the same algorithm or software to design the primers and probes. For optimal results, only combine assays that have been designed using the same parameters.

Check the functionality of each set of primers and probes in individual assays before combining the different sets in the multiplex assay. Choose compatible reporters and quenchers based on a specific instrument. See How do I select appropriate reporter and quencher combinations for multiplex PCR.

FAQ ID -9093

QuantiFast Probe Assays are only sold in combination with optimized real-time RT-PCR master mixes and cannot be sold as stand-alone assays.

For one-step RT-PCR with singleplex detection: QuantiFast Probe RT-PCR Plus Kit
For one-step RT-PCR with duplex detection: QuantiFast Probe RT-PCR Plus Kit
For two-step RT-PCR with singleplex detection: QuantiFast Probe PCR Kit
For two-step RT-PCR with duplex detection: QuantiFast Multiplex PCR Kit

FAQ ID -2360

SYBR Green dye does not interfere with ethidium bromide staining, and realtime SYBR Green PCR products can be visualized on an agarose gel.

FAQ ID -312

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.

QuantiTect Primer Assays are primer sets for use in SYBR Green based real-time RT-PCR analysis.
QuantiFast Probe Assays are primer-probe sets for use in dual-labeled 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

In one-step RT-PCR, both reverse transcription and amplification are performed in the same tube. Upon completion of reverse transcription, the reaction temperature is raised to reach denaturation/PCR enzyme activation temperature and the thermal cycling (PCR) begins. One-step RT-PCR generally uses gene-specific primers for both the RT and PCR steps. The procedure is fast, easy to automate, and minimizes the risk of contamination due to fewer handling steps.

In two-step RT-PCR, the RNA is first transcribed into cDNA using oligo-dT primers, random oligos, or gene-specific primers. An aliquot of the RT reaction is subsequently added to the real-time PCR reaction in a second tube. Choice of different types of RT primers allows the analysis of different transcripts by PCR from one RT reaction. Most commonly, an oligo-dT primer is used for the RT step, followed by PCR with a pair of gene-specific primers. Precious RNA samples can be immediately transcribed into more stable cDNA for later use and long-term storage.

The advantages of each method are summarized below:

Two-step RT-PCR	One-step RT-PCR
Multiple PCRs from one RT reaction	Easy handling
Flexibility with RT primer choice	Fast procedure
Enables long-term storage of cDNA	High reproducibility
	Low contamination risk

Optimized one-step and two-step RT-PCR kits compatible with any real-time cycler are available from QIAGEN. For further details, please see our online section on 'Critical factors for successful gene expression assays', or download our Brochure 'Critical Factors for Successful Real-Time PCR'.

FAQ ID -1056

No. Due to hardware limitations, the maximum capacity of these real-time cyclers is triplex PCR.

FAQ ID -716

This depends on the amount of contaminating amplicon. If the contamination is high (e.g., 10e6 copies), then there will still be traces of amplicon remaining. However, we expect a reduction by a factor of around 1000 using QuantiTect +UNG Kits (i.e., after UNG pretreatment, only 0.1% of the initial contamination will still be present in the reaction).

FAQ ID -2139

The reduced reaction volume recommended for QuantiFast PCR Kits compared to QuantiTect PCR Kits allows more efficient temperature transfer during short cycling steps.

FAQ ID -1447

The presence of ROX as passive reference dye in the Master Mix of the QuantiTect Multiplex PCR Kit and the QuantiFast Mutliplex PCR Kit limits the use of these kits to triplex PCR on 4-channel real-time cyclers. This is because the ROX dye occupies the channel for detecting probes labeled with ROX, Texas Red, or other equivalent dyes.

However, 4-plex PCR is possible on on instruments equipped with at least 5 channels. Alternatively, if you have a 4-channel real-time cycler that does not use ROX passive reference dye (e.g., iCycler iQ, Rotor-Gene 3000, Mx4000, Mx3000P, Smart Cycler II, LightCycler 2.0), you can use the QuantiTect Multiplex PCR NoROX Kit or the QuantiFast Multiplex PCR +R Kit to perform 4-plex PCR.

Please see table “Real-Time, Multiplex PCR on a Wide Range of Real-Time Cyclers” for compabilities of the QuantiTect Multiplex kits with different real-time cyclers.

FAQ ID -715

Replicates in real-time PCR may have different plateau heights due to differences in the reaction kinetics for each sample. Even though replicates start out with identical template amounts, the rate at which reagents are being depleted, and the point when exponential accumulation of PCR product stops and becomes linear, differ between replicates. This will result in different plateau heights, the stage where PCR reactions have come to a halt, and little or no additional PCR product is being amplified. You can find further information in Chapter 'Quantification of target amounts' of our Brochure "Critical Factors for Successful Real-Time PCR".

FAQ ID -539

Fluorescent oligonucleotides should be stored in the dark, as light can slowly degrade the fluorescent moieties. For optimal long-term storage of fluorescent dye-labeled probes (except Cyanine 570, Cy3.5, Cyanine 670, and Cy5.5), the oligos should be resuspended in a slightly basic solution (e.g., TE buffer at pH 8.0). If resuspended below pH 7.0, the probe can degrade. We recommend to aliquot the sample, and store the aliquots at -20°C.

Note that Cyanine 570, Cy3.5, Cyanine 670, and Cy5.5 begin to degrade at a pH above pH 7.0. For best results, resuspend Cy-labeled oligos at pH 7.0, aliquot, lyophilize, and store at -20°C.

FAQ ID -784

The ice step is recommended to prevent non-specific reverse transcription during reaction set-up. Mispriming by Taq is not a concern in these cases because both QuantiTect RT-PCR and PCR kits contain HotStarTaq, a DNA polymerase that only becomes active following a 15 minute, 95 degree incubation step.

FAQ ID -283

No. The master mixes in Rotor-Gene Kits contain dTTP instead of dUTP. If UNG treatment is required, we recommend using QuantiTect +UNG Kits. QuantiTect Kits are also compatible with the Rotor-Gene Q; however, the kits require a significantly longer cycling time.

FAQ ID -2117

Yes. The pre-optimized master mix ensures that all gene targets in a multiplex reaction are amplified with the same efficiency and sensitivity as in corresponding "single-plex" reactions, independent of starting copy numbers.

FAQ ID -718

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:

Remove a single aliquot of water from your PCR-grade stock, sufficient to complete the experiment. This minimizes the number of times that the stock container is opened, thereby minimizing contamination risks.
Use only fresh PCR-grade reagents and disposable labware.
Treat any labware (tubes, tips, and tip boxes) used in PCR with 10% bleach, before discarding.
Maintain a dedicated workspace for PCR setup (perhaps a PCR-only hood), away from areas of the lab where post-PCR work is done, such as running gels, enzyme digestions, and cloning.
Change the lab bench pads/papers often and decontaminate lab benches and labware (racks, pipettors, etc.) before each use by washing with 10% bleach, and/or exposing to UV light for at least 10 minutes. This serves to degrade and/or inactivate contaminating DNA.
Before, during, and after the experiment, minimize the opening and closing of any tubes or plates used during the experiment.

FAQ ID -2654

For accurate quantification we recommend an amplicon length of 100-150 bp to ensure optimal amplification efficiency.

FAQ ID -553

QuantiTect Kits for real-time PCR and RT-PCR have been optimized for a final reaction volume of 50 µl for use with single tubes and 96-well plates, or 20 µl for use with 384-well plates and LightCycler capillaries. We strongly recommend using the primer and probe concentrations, reaction volumes, and amount of starting template given in the QuantiTect handbooks. However, volumes may be reduced to 20 µl and 10 µl, respectively.

FAQ ID -551

Recombinant DNA (recDNA) is very stable and represents the average size of mRNA. Due to the cloning and purification processes, obtaining recDNA can lengthen the overall process of generating standards.

Recombinant RNA (recRNA) and native RNA undergo reverse transcription as well as PCR, and mimic the natural process for mRNA in RT-PCR. Complicated cloning and purification of recRNA and instability of recRNA are two disadvantages for using recRNA as a standard. For further details please refer to the section "Generating Standard Curves" in Appendix D of the QuantiTect SYBR Green PCR Handbook.

FAQ ID -729

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.

FAQ ID -1141

The primers of the QuantiTect Primer Assays are at a proprietary concentration that was specially optimized for sensitive and efficient amplification in any real time cycler. Always dilute these primers to a final work solution of 1x in your reaction, using either the QuantiTect SYBR Green PCR Kit or the QuantiTect SYBR Green RT-PCR Kit. Follow the instructions for use of the Primer Assays in the QuantiTect Primer Assay handbook.

FAQ ID -850

No. UNG treatment does not provide any advantage for the QuantiFast and Rotor-Gene PCR kits because the mastermixes do not contain dUTP. Use the QuantiTect kits if you intend to use the UNG treatment.

FAQ ID -9092

Yes. The QuantiTect Master Mix may not necessarily freeze at -20 degrees. The performance is not affected as long as the correct storage temperature is maintained.

-20

Quenched FRET assays are similar to FRET assays except that the decrease in energy of the donor fluorophore is measured instead of the increase in energy of the acceptor fluorophore.

FAQ ID -542

The number of template copies that can be detected during real-time PCR depends on template and primer quality, as well as on the amplification reagents used. As few as 10 copies can typically be detected with the QuantiTect Probe PCR and QuantiTect SYBR Green PCR Kits.

FAQ ID -543

The annealing temperature for QuantiTect Primer Assays should be 55^oC when used with the QuantiTect SYBR Green PCR Kit and the QuantiTect SYBR Green RT-PCR Kit.

Use of the QuantiFast SYBR Green PCR and QuantiFast SYBR Green RT-PCR Kits requires a combined annealing/extension step at 60^oC, as described in the QuantiTect Primer Assay Handbook.

Note that these Assays are guaranteed for use with the QuantiTect or QuantiFast chemistries only!

FAQ ID -849

The storage time for QuantiFast PCR Kits is shorter than for QuantiTect PCR Kits, because all QuantiFast master mixes contain HotStarTaq Plus DNA Polymerase, instead of HotStarTaq DNA Polymerase which requires longer activation times.

Excessive exposure to elevated temperatures will result in reactivation of the HotStarTaq Plus DNA Polymerase, eventually leading to nonspecific amplification.

FAQ ID -1446

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.

FAQ ID -90990

The REST 2009 (Relative Expression Software Tool) software applies mathematic models that compensate for the different PCR efficiencies of the gene of interest and reference genes. In addition, the software can use multiple reference gene normalization to improve the reliability of result, as well as provides statistical information suitable for robust comparison of expression in groups of treated and untreated. QIAGEN offers the REST 2009 software free of charge.

FAQ ID -9095

Yes, QuantiTect Primer Assays work very well under fast-cycling conditions. Results achieved with QuantiFast SYBR Green Kits are comparable to those achieved with QuantiTect SYBR Green Kits.

FAQ ID -1714

No, UNG is only available in combination with a QuantiTect PCR Kit.

FAQ ID -2134

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

During the late phase of PCR, as a lot of PCR product has been generated, there is strong competition between hybridization of the probe to the target strand and re-association of the two complementary product strands. For some primer–probe combinations, re-association occurs more quickly than probe hybridization towards the end of the PCR. Therefore, the yield of PCR product seems to decrease after reaching a peak. For accurate quantification, fluorescence data is measured during the log-linear phase of the reaction, i.e., during the initial increase of fluorescence, before this phenomenon occurs.

FAQ ID -587

For each QuantiTect Primer Assay, we retrieve the sequence of the target gene from curated databases and exclude SNP regions from assay design.

We then use our proprietary algorithm to design assays that amplify RNA sequences only (i.e., at least one primer overlaps a splice site), provided that information on the position of splice sites is available. The assays are designed to provide optimal performance with QuantiFast and QuantiTect SYBR Green Kits.

After assay design, we validate randomly selected QuantiTect Primer Assays using real-time RT-PCR to check their compatibility with various real-time cyclers. Both two-step and one-step RT-PCR are carried out. Successful amplification of the target is indicated by the following factors: high sensitivity, high efficiency, high specificity (i.e., a single peak in melting curve analysis), and no primer–dimers in the no-template control (NTC).

To find a QuantiTect Primer Assay for your target gene of interest, please visit our GeneGlobe data base.

FAQ ID -1982

No, that is not necessary. Simply use the primer concentrations specified in the protocols in the supplied QuantiTect Multiplex PCR handbooks.

FAQ ID -714

Check the template quality and integrity by amplifying an endogenous control gene. Check the amplicon by QIAxcel Advanced system or agarose gel electrophoresis to show that amplification was successful.

Determine whether the gene of interest is expressed in your sample. See How can I find out if my gene of interest is express in a specific tissue type or cell line. Ensure the assay setup and cycling conditions are correct, and that the data collection channel matches the emission wavelength of the fluorescent dye used. Use a control sample in which the gene of interest is definitely expressed.

If the issue persists, please send the original run file to QIAGEN Technical Services.

FAQ ID -9091

QuantiTect Primer Assays are optimized for an annealing temperature of 55ºC when using the QuantiTect SYBR Green PCR Kit (for two-step RT-PCR) or the QuantiTect SYBR Green RT-PCR Kit (for one-step RT-PCR) .

Increasing the annealing temperature will reduce PCR performance (sensitivity and PCR efficiency) when using QuantiTect Primer Assays with these kits.

FAQ ID -1146

Yes, please follow the Supplementary Protocol 'Performing quantitative, real-time, duplex, triplex, or 4-plex PCR on the LightCycler 2.0 system using the QuantiTect Multiplex PCR NoROX Kit' (PCR44).

FAQ ID -966

For duplex analysis, using non-fluorescent quenchers (e.g., Black Hole Quencher^®) is preferred over fluorescent quenchers (e.g., TAMRA fluorescent dye). For triplex and 4-plex analysis, QIAGEN strongly recommends using non-fluorescent quenchers. Generally, use the green channel, the yellow channel, and the orange and crimson channels to detect the least abundant target, the second least abundant target, and the two most abundant targets, respectively. For instrument-specific recommendations, please see the handbooks for the QuantiTect Multiplex PCR kit, QuantiFast Multiplex kit or Rotor-Gene Multiplex kit.

FAQ ID -9094

Yes, please follow the Supplementary Protocol 'Adding new reporter dyes to the ABI PRISM 7900 Sequence Detection System for use in quantitative, real-time, triplex PCR with the QuantiTect Multiplex PCR Kit' (PCR43).

FAQ ID -965

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%

FAQ ID -2688

The gDNA wipeout buffer incubation step can be skipped when the total RNA is free from genomic DNA. However, the gDNA wipeout buffer is still required to be added because the reverse transcription step is optimized in the presence of components in the gDNA wipeout buffer.

FAQ ID -9098

Make sure that template, primers, probes, and amplification reagents are stored correctly and avoid multiple freeze–thaw cycles for oligonucleotides and template. Check the performance of your real-time instrument as some instruments require the halogen lamp to be frequently replaced. Lasers must also be replaced occasionally.

FAQ ID -589

In quantitative (real-time) PCR, primer-dimers will appear as a peak with a Tm lower than the Tm of the specific product. This peak will also appear in the no-template control (NTC). In non-quantitative endpoint PCR, primer dimer will appear as a more or less faint smear on an agarose gel, below the product band of interest.

FAQ ID -552

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.

FAQ ID -2678

We highly recommend any QuantiTect or QuantiFast Kit for quantitative PCR on cDNA generated with the QuantiTect Whole Transcriptome Kit.

FAQ ID -1592

Depending on the qPCR instrument, time savings when switching from standard cycling (e.g., QuantiTect PCR Kits) to fast cycling using QuantiFast Kits range from 40% to 60%.

FAQ ID -1438

Even when detecting low-abundance targets, we recommend using no more than 500 ng/reaction of DNA (for PCR kits) or RNA (for RT-PCR kits). Generally, 1–100 ng template should be sufficient and for abundant transcripts as little as 1 pg can be used.

Template purity is important if large volumes of low concentration template are to be added to the reaction. Using DNA or RNA purified with QIAGEN products, the template can contribute up to 40% of the final reaction volume as long as the recommended template amounts are not exceeded. If cDNA from an RT reaction is used as template, the volume of undiluted RT reaction added should not exceed 10% of the final PCR volume.

FAQ ID -1086

Store the standards at a high concentration in aliquots at -20^oC to -70^oC. If using low concentrations, stabilize standards with carrier nucleic acid. It is always best to use freshly diluted standards for each experiment. If possible, use siliconized tubes for standard (and target) dilutions. This will prevent any unspecific binding of nucleic acids to the plastic.

FAQ ID -9099

The LightCycler 2.0 requires a color compensation file to separate the fluorescent signals and eliminate crosstalk between the individual detection channels. Please contact QIAGEN Technical Services for a specialized protocol.

FAQ ID -780

Reliable HRM analysis results depend on template quality, highly specific HRM PCR kit with a saturation dye, a real-time instrument with HRM capability, and powerful software package. Factors critical for successful HRM analysis are:

Use the same genomic DNA purification procedure for all samples being analyzed by HRM. This avoids variation due to differing composition of elution buffers.
DNA template concentrations should be normalized using the same dilution buffer. Ensure the C_T values are below 30 and differ no more than 3 C_T values across individual samples.
Design assays with amplicon length 70–350 bp. For SNP analysis, use amplicon length 70–150 bp.
Always start with 0.7 µM primer concentration

For more details, please refer to the HRM Technology – FAQs and the Critical Success Factor for HRM performance.

FAQ ID -9097

No, QuantiTect Primer Assays are supplied as lyophilized, premixed primer pairs. Reaction components for SYBR Green real-time RT-PCR must be purchased separately.

For two-step RT-PCR, the QuantiTect Reverse Transcription Kit and QuantiTect SYBR Green PCR Kit are recommended
For one-step RT-PCR, the QuantiTect SYBR Green RT-PCR Kit is recommended

To find a QuantiTect Primer Assay for your target gene of interest, please visit our GeneGlobe data base.

FAQ ID -1143

Compatible reporter dye combinations for different real-time cyclers are listed in the "Important Notes" section under 'Suitable combinations of reporter dyes' in the QuantiTect Multiplex PCR Handbook and the QuantiTect Multiplex PCR NoROX Handbook.

FAQ ID -719

No. In fact, QuantiTect SYBR Green PCR Kits contain a stabilization reagent that increases the sensitivity of real-time PCR. The QuantiTect SYBR Green Kits also contain a carefully controlled concentration of SYBR Green that is sufficient to detect PCR fragments while having no inhibitory effect on the enzymatic reaction.

FAQ ID -328

Shorter amplification products facilitate high PCR efficiencies. Ideally, amplicon length should be less than 150 bp for optimal amplification efficiency. PCR efficiencies close to 100% are a crucial prerequisite for accurate quantification of target copy numbers in real-time PCR.

FAQ ID-751

For quantification of RNA, we strongly recommend using RNA molecules as standards. Use of in vitro transcripts as standards takes into account the variable efficiency of the RT reaction. An alternative to the use of in vitro transcripts as RNA standards is the use of a defined RNA preparation (e.g., from a cell line or virus preparation), for which the absolute concentration of the target has already been determined.

For quantification of DNA, several types of DNA can be used, such as plasmids, PCR products, or genomic DNA.

For more information, see Appendix E 'Generating Standard Curves' in the QuantiTect Probe PCR Handbook.

FAQ ID -1085

QuantiTect PCR +UNG Kits are available as 200-reaction kits only.

FAQ ID -2136

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.

FAQ ID -2119

Yes, probes and primers can be added to the QuantiTect Probe PCR- and the QuantiTect Probe RT-PCR Master Mix. This master mix can be stored at -20°C for up to 50 days, with a maximum of six freeze-thaw cycles (tested in our labs).

The master mix must be stored protected from light to avoid bleaching of the fluorescent probe. However, the QuantiTect RT Mix should be stored separately at –20°C, because the reverse transcriptases are sensitive to freezing in an aqueous environment. The QuantiTect RT Mix should be added to this master mix just prior to adding the template RNA and placing the reactions into the thermal cycler.

FAQ ID -584

We have compared QuantiFast Kits and QuantiTect Kits using around 30 different assays (using both SYBR Green and Probe detection for each assay).

QuantiFast Kits gave identical or sometimes better Ct values than QuantiTect Kits (except for very long amplicons). Therefore, scientists switching from QuantiTect to QuantiFast Kits can, in most cases, obtain comparable results.

FAQ ID -1441

Yes - dTTP in the QuantiTect Master Mix in QuantiTect SYBR Green and Probe PCR Kits is partially substituted by dUTP, therefore allowing treatment with uracil-N-glycosylase.

However, only heat-labile UNG can be used for one-step RT-PCR with the QuantiTect Probe RT-PCR and SYBR Green RT-PCR Kits. This is because heat stable UNG (isolated from E. coli) will destroy any cDNA synthesized during the RT step at 50°C. Heat-labile UNG will have lost any activity after a few minutes of the RT-step and therefore cannot interfere with cDNA synthesis.

For heat-stable uracil-N-glycosylase, please use the QuantiTect SYBR Green PCR +UNG (cat. no. 204163) or QuantiTect Probe PCR +UNG Kits (cat. no. 204363). Both kits include heat-stabile uracil-N-glycosylase. Although QIAGEN UNG is inactivated by incubation at 95°C for 15 minutes, the enzyme may exhibit residual activity at lower temperatures due to refolding. Therefore, it is recommended to perform subsequent PCR using a temperature of 55°C or above for the annealing step.

FAQ ID -564

LightCycler: We do not recommend performing real-time, multiplex PCR using TaqMan® probes or QuantiTect Assays on the LightCycler system due to the limitations of its optical detection system.
LightCycler 2.0: Information on using the QuantiTect Multiplex PCR NoROX Kit with the LightCycler 2.0 system is provided in the QuantiTect Multiplex PCR NoROX Handbook. You will find the recommendation for the LightCycler 2.0 system in the chapter 'Important Notes' under "Suitable combinations of reporter dyes".

See trademarks.

FAQ ID -717

Depending on primer design and copy number of target, primer-dimer may occur and its signal might be detected. Typical strategies against this are to optimize PCR conditions and/or redesign the assay.

Alternatively, an additional data-acquisition step can be added to the 3-step cycling protocol. First, determine the melting temperatures (T_m) for both the amplicon and the primer-dimer. Then, add a 15 second data-acquisition step with a temperature that is higher than the primer-dimer T_m, but approximately 3ºC lower than the specific amplicon T_m.

FAQ ID -9096

The Rn value, or normalized reporter value, is the fluorescent signal from SYBR Green normalized to (divided by) the signal of the passive reference dye for a given reaction. The delta Rn value is the Rn value of an experimental reaction minus the Rn value of the baseline signal generated by the instrument. This parameter reliably calculates the magnitude of the specific signal generated from a given set of PCR conditions. For more information, please refer to your cycler's user manual.

FAQ ID -2681

The emission maximum of Yakima Yellow (552 nm) is almost identical to that of the fluorescent dye VIC. Therefore, the channel and filter settings for VIC can also be used for Yakima Yellow.

FAQ ID -540

The melting temperature of a PCR product depends on the salt concentration of the buffers used for amplification. Buffer compositions differ between QuantiTect SYBR Green PCR Kits and Roche kits, resulting in different PCR product melting temperatures.

FAQ ID -1084

FAQ ID -2690