SYBR Premix Ex Taq II (Tli RNaseH Plus)

Transcription

1 For Research Use SYBR Premix Ex Taq II (Tli RNaseH Plus) Product Manual

2 Table of Contents I. Description... 3 II. Principle... 3 III. Kit components... 4 IV. Materials Required but not Provided... 4 V. Storage... 5 VI. Precautions... 5 VII. Protocol... 6 VIII. Optimization...10 IX. Appendix...12 X. Quality specification...14 XI. Related products...15 XII. Note URL:

3 I. Description SYBR Premix Ex Taq II(Tli RNaseH Plus) is a reagent specifically designed for intercalator-based real time PCR using SYBR Green I *1. It is supplied at a 2 concentration premixed with SYBR Green I at a concentration appropriate for real time monitoring, making it easy to prepare reaction mixtures. The 2 premixed reagent also contains Tli RNaseH, a heat-resistant RNase H, which minimizes inhibition of PCR due to residual mrna when using cdna as template. This product, with a modified buffer composition, offers a higher reaction specificity than that by SYBR Premix Ex Taq (Tli RNaseH Plus) (Cat. #RR420A). With inhibition of non-specific amplifications, which interfere with quantitative determination, accurate assays over a wide range are possible. A combination of this buffer and TaKaRa Ex Taq HS, a hot start PCR enzyme that uses an anti-taq antibody, allows highly reproducible and reliable real time PCR analyses. Benefits : (1) Allows rapid and accurate detection and assay of genes by real time PCR (2) It is supplied at a 2 concentration premixed with SYBR Green I. Simply add primers, template, and sterile distilled water to perform intercalator-based real time PCR. (3) TaKaRa Ex Taq HS, a hot start PCR enzyme, is used for PCR. The buffer system has been optimized for real time PCR, allowing good amplification efficiency and highsensitivity detection. (4) The 2 reagent is premixed with Tli RNaseH, a heat-resistant RNaseH. It minimizes inhibition of PCR due to residual mrna when using cdna as template. II. Principle *1: TAKARA BIO is under a license agreement with Molecular Probes Inc. for the use of SYBR Green I as a reagent for research purposes. SYBR is a registered trademark of Molecular Probes Inc. This product performs PCR amplifications with TaKaRa Ex Taq HS. PCR amplification products may be monitored in real time by SYBR Green I. 1. PCR PCR is a technique used to amplify only the target gene fragment from a minute amount of DNA. By repeating 3-step cycles of DNA heat denaturation, primer annealing and elongation, the target gene fragment may be amplified up to a million times by DNA polymerase within a short time. This product uses TaKaRa Ex Taq HS, a hot start PCR enzyme, for amplifications, allowing the prevention of non-specific amplifications derived from mispriming or primer dimer formation during reaction mixture preparation or other pre-cycling steps and making high-sensitivity detection possible. URL: 3

4 2. Fluorescent detection - Intercalator method This method involves the addition of a reagent (intercalator: e.g., SYBR Green I) that emits fluorescence when bound to double-strand DNA to reaction mixtures, allowing the detection of fluorescence associated with amplification. Measuring the fluorescence intensity not only allows quantitative determination but also provides the melting temperature of amplified DNA. Figure 1. Fluorescent intercalator detection method. III. Kit components [for µl reactions] SYBR Premix Ex Taq II (Tli RNaseH Plus) (2 conc.) *1 1 ml ROX Reference Dye (50 conc.)* 2 40 µl ROX Reference Dye II (50 conc.) *2 40 µl *1: Contains TaKaRa Ex Taq HS, dntp Mixture, Mg 2+, Tli RNaseH and SYBR Green I * For this product's quality specification, please refer to Section X. *2: This component is to be used for analyses using a device that corrects fluorescent signals between wells such as the real-time PCR device by Applied Biosystems. Please use ROX Reference Dye for Applied Biosystems 7300 Real- Time PCR System or StepOnePlus and ROX Reference Dye II for 7500/7500 Fast Real-Time PCR System. This component is not required with Thermal Cycler Dice Real Time System II or LightCycler. IV. Materials Required but not Provided 1. Reagents - Primers for PCR For designing real time PCR primers, please refer to Section IX.1. - Sterile distilled water 4 URL:

5 2. Materials - Special reaction tubes or plates - Micropipettes and tips (autoclave treated) - Gene amplification system for real time PCR (authorized instruments) Compatible instruments include: Thermal Cycler Dice Real Time System II (Cat. #TP900/TP960) Applied Biosystems 7300/7500 Real-Time PCR System, 7500 Fast Real-Time PCR System, StepOnePlus Real-Time PCR System (Applied Biosystems) LightCycler (Roche Diagnostics) Note: We recommend using SYBR Premix Ex Taq (Tli RNaseH Plus) (Cat. #RR420A) for Smart Cycler System/Smart Cycler II System (Cepheid). V. Storage 4 Note: VI. Precautions Product is stable for up to 6 months when stored at 4. Protect this kit from light and avoid contamination. This kit is shipped in a dry ice-packed package. Store the kit protected from light at 4 after its receipt. For long-term storage, keep it at -80. (Do not store at -20 ) Store a thawed product at 4 and use it within 6 months. Read these precautions before use and follow them when using this product. 1. Before use, make sure the reagent is evenly mixed by gently turning it upside down several times without creating bubbles. Uneven reagent composition will result in inadequate reactivity. Do not mix by vortexing. When stored at -80, SYBR Premix Ex Taq II (2 conc.) may develop a white to pale yellow precipitate. Gently warm it with hands and let stand protected from light at room temperature for a while, followed by turning it upside down several times to dissolve the precipitate completely. The presence of precipitate is indicative of uneven reagent composition; make sure the reagent is evenly mixed before use. 2. Place reagents on ice when preparing the reaction mixture. 3. This product contains SYBR Green I. Take care to avoid exposures to strong light when preparing the reaction mixture. 4. Make sure to use fresh disposable tips to avoid any potential contamination between samples when preparing or dispensing reaction mixtures. URL: 5

6 VII. Protocol 1. Protocol when using Thermal Cycler Dice Real Time System II A. Prepare the PCR mixture shown below. <Per reaction> Reagent Amount Final conc. SYBR Premix Ex Taq II (2 ) 12.5 µl 1 PCR Forward Primer (10 µm) 1.0 µl 0.4 µm *1 PCR Reverse Primer (10 µm) 1.0 µl 0.4 µm *1 template (<100 ng)* µl dh2o (sterile distilled water) 8.5 µl total 25 µl *3 *1: A final primer concentration of 0.4 µm is most likely to yield a good result. Nevertheless, if there is an issue with reactivity, try to find an optimal concentration between 0.2 and 1.0 µm. *2: The quantity to be used varies depending on the number of target copies present in the template solution. Make serial dilutions to determine what an appropriate amount is. It is preferable to use no more than 100 ng of DNA template. Furthermore, if cdna (RT reaction mixture) is used as template, the volume of the PCR mixture should be no more than 10%. *3: The recommended reaction volume is 25 µl. B. Initiate the reaction. The shuttle PCR standard protocol is recommended for PCR. Try this protocol first and optimize PCR conditions as necessary. Perform a 3-step PCR when using a primer with low T m value or when a shuttle PCR is not feasible. Note: TaKaRa Ex Taq HS in this kit is a hot start PCR enzyme with an anti-taq antibody that inhibits polymerase activity. The initial denaturation step prior to PCR should be at 95 for 30 sec. Enzyme activity decreases with longer heat treatment and the amplification efficiency and quantification accuracy can be affected. Even for the initial denaturation of template before PCR, 95 for 30 sec is generally sufficient. Hold (initial denaturation) Cycle: sec 2 Step PCR *4 Cycle: 40 95, 5 sec 60, sec Dissociation Figure 2. Shuttle PCR standard protocol. *4: For optimizing PCR conditions, please refer to Section VIII. 6 URL:

7 C. After the reaction is complete, check the amplification and melting curves and plot a standard curve if an assay will be performed. When using Thermal Cycler Dice Real Time System II, please refer to its instruction manual to read analytical methods. 2. Protocol when using Applied Biosystems 7300/7500/7500 Fast Real-Time PCR System and StepOnePlus Real-Time PCR System * Please follow the procedures provided in the manual of the respective instrument. A. Prepare the PCR mixture shown below. <Per reaction> Reagent Amount Amount Final conc. SYBR Premix Ex Taq II (2 ) 10 µl 25 µl 1 PCR Forward Primer (10 µm) 0.8 µl 2 µl 0.4 µm *1 PCR Reverse Primer (10 µm) 0.8 µl 2 µl 0.4 µm *1 ROX Reference Dye (50 ) or Dye II (50 )* µl 1 µl 1 template (<100 ng)* µl 4 µl dh2o (sterile distilled water) 6.0 µl 16 µl total 20 µl *4 50 µl *4 *1: A final primer concentration of 0.4 µm is most likely to yield a good result. Nevertheless, if there is an issue with reactivity, try to find an optimal concentration between 0.2 and 1.0 µm. *2: The concentration for ROX Reference Dye II (50 ) is lower than that for ROX Reference Dye (50 ). Use ROX Reference Dye II (50 ) when performing analyses with Applied Biosystems 7500 Real-Time PCR System or 7500 Fast Real-Time PCR System. Use ROX Reference Dye (50 ) when using StepOnePlus and 7300 Real-Time PCR System. *3: The quantity to be used varies depending on the number of target copies present in the template solution. Make serial dilutions to determine what an appropriate amount is. It is preferable to use no more than 100 ng of DNA template per 20 µl. Furthermore, if cdna (RT reaction mixture) is added as template in an RT-PCR, the volume of the PCR mixture should be no more than 10%. *4: Prepare in accordance with the recommended volume for each instrument. URL: 7

8 B. Initiate the reaction. The recommended protocol for PCR is the shuttle PCR standard protocol described below. Try this protocol first and optimize PCR conditions as necessary. Perform a 3-step PCR when using a primer with low T m value or when a shuttle PCR is not feasible. (For optimizing PCR conditions, please refer to Section VIII.) 1) Applied Biosystems 7300/7500 Real-Time PCR System, StepOnePlus Stage 1: Initial denaturation Reps: 1 95, 30 sec Stage 2: PCR Reps:40 95, 5 sec 60, sec* Dissociation stage Figure 3. Shuttle PCR standard protocol. 2) Applied Biosystems 7500 Fast Real-Time PCR System Shuttle PCR standard protocol Holding Stage Reps: 1 95, 30 sec Cycling Stage Number of Cycles: 40 95, 3 sec 60, 30 sec Melt Curve Stage * : With StepOnePlus, set to 30 sec; with 7300, set to 31 sec; and with 7500, set to 34 sec. Note: TaKaRa Ex Taq HS in this kit is a hot start PCR enzyme with an anti-taq antibody that inhibits polymerase activity. the initial denaturation step prior to PCR should be at 95 for 30 sec. Enzyme activity decreases with longer heat treatment and the amplification efficiency and quantification accuracy can be affected. Even for the initial denaturation of template before PCR, 95 for 30 sec is generally sufficient. C. After the reaction is complete, check the amplification and melting curves and plot a standard curve if an assay will be performed. Please refer to the instruction manual for real time PCR instrument to read about analytical methods. 8 URL:

9 3. Protocol when using LightCycler * Please follow the procedures provided in the LightCycler manual (Roche Diagnostics). A. Prepare the PCR mixture shown below. <Per reaction> Reagent Amount Final conc. SYBR Premix Ex Taq II (2 ) 10 µl 1 PCR Forward Primer (10 µm) 0.8 µl 0.4 µm *1 PCR Reverse Primer (10 µm) 0.8 µl 0.4 µm *1 template (<100 ng)* µl dh2o (sterile distilled water) 6.4 µl total 20 µl *1: A final primer concentration of 0.4 µm is most likely to yield a good result. Nevertheless, if there is an issue with reactivity, try to find an optimal concentration between 0.2 and 1.0 µm. *2: The quantity to be used varies depending on the number of target copies present in the template solution. Make serial dilutions to determine what an appropriate amount is. It is preferable to use no more than 100 ng of DNA template. Furthermore, if cdna (RT reaction mixture) is added as template in an RT-PCR, the volume of the PCR mixture should be no more than 10%. B. Briefly centrifuge PCR capillaries and set them in LightCycler to initiate the reaction. The recommended protocol for PCR is the shuttle PCR standard protocol described below. Try this protocol first and optimize PCR conditions as necessary. Perform a 3-step PCR when using a primer with low T m value or when a shuttle PCR is not feasible. (For optimizing PCR conditions, please refer to Section VIII.) Stage 1: Initial denaturation 95, 30 sec 20 /sec 1 cycle Stage 2: PCR 95, 5 sec 20 /sec 60, 20 sec 20 /sec 40 cycles Stage 3: Melting curve analysis 95, 0 sec 20 /sec 65, 15 sec 20 /sec 95, 0 sec 0.1 /sec Figure 4. Shuttle PCR standard protocol. URL: 9

10 VIII. Optimization Note: TaKaRa Ex Taq HS is a hot start PCR enzyme with an anti-taq antibody that inhibits polymerase activity. The initial denaturation step prior to PCR should be at 95 for 30 sec. Enzyme activity decreases with longer heat treatment and the amplification efficiency and quantification accuracy can be affected. Even for the initial template denaturation before PCR, 95 for 30 sec is generally sufficient. C. After the reaction is complete, check the amplification and melting curves and plot a standard curve if an assay will be performed. Please refer to the instruction manual for your real time PCR instrument to read about analytical methods. If the recommended condition (shuttle PCR standard protocol) provided unsatisfactory reactivity, follow the procedures below to evaluate what primer concentration and PCR condition to use. In addition, depending on the reaction system, switching to a real time PCR reagent from another type of Perfect Real Time series (Cat. #RR420A/B, RR091A/B) may greatly improve the reactivity. Selecting PCR conditions based on a comprehensive analysis by taking into consideration both reaction specificity and amplification efficiency. A PCR system well balanced between these two aspects allows accurate assays over a wide range of concentrations. System with a high reaction specificity With no template control, non-specific amplifications such as primer-dimer formation do not take place. Non-specific amplification products, those other than the target product, are not generated. System with a high amplification efficiency Amplification product is detected at earlier cycles (small C t value). PCR amplification efficiency is high (near the theoretical value of 100%). 1. Evaluation of primer concentration The relationships between primer concentration and reaction specificity and amplification efficiency are as follows. Reducing the primer concentration raises reaction specificities. Increasing the primer concentration, on the other hand, raises amplification efficiencies. (Primer concentration) Low (0.2 µm) High (1.0 µm) Specificity high low Efficiency low high 10 URL:

11 2. Evaluation of PCR condition To raise reaction specificity Raising the annealing temperature may improve reaction specificities. Perform optimization while checking the balance with respect to amplification efficiency. [Shuttle PCR] Standard protocol 95 5 sec sec Raise the annealing temperature 95 5 sec up to sec To raise amplification efficiency Prolonging the elongation time or switching to a 3-step PCR may improve amplification efficiencies. Perform optimization using the steps below. [Shuttle PCR] Standard protocol Prolong the elongation time [3-step PCR] Prolong the elongation time 95 5 sec sec 95 5 sec 60 1 min sec sec sec 95 5 sec sec 72 1 min - Initial denaturation Generally, 95 for 30 sec is sufficient for initial denaturation procedures. This condition offers good reactivity in most cases, even with difficult to denature templates such as circular plasmids and genomic DNA. This procedure may be extended to 1 to 2 minutes at 95 depending on the template. Prolonging this procedure for too long may inactivate the enzyme. Therefore, it is recommended to heat for no more than 2 minutes. 3. Relationship between reagent and reactivity TAKARA BIO supplies three different real-time PCR reagents for SYBR Green Assay. Their respective relationships with reaction specificity and amplification efficiency are as follows. SYBR Premix Ex Taq (Tli RNaseH Plus) (Cat. #RR420A/B) provides a high amplification efficiency. SYBR Premix Ex Taq II (Tli RNaseH Plus) (Cat. #RR820A/B) and SYBR Premix DimerEraser (Perfect Real Time) (Cat. #RR091A/B) are effective in raising the reaction specificity, (Reagent) SYBR Premix Ex Taq SYBR Premix Ex Taq II SYBR Premix DimerEraser Specificity lower higher Efficiency higher lower URL: 11

12 IX. Appendix 1. Primer design Designing a primer with a good reactivity is critical to efficient real time PCR. Please follow the guideline below to design a primer that gives a high amplification efficiency without non-specific reactions. RT-PCR primers designed and synthesized using this system allow reactions based on the shuttle PCR standard protocol (Section VII). Amplification product Amplif ication size Primer The optimum size is bp (amplification is possible for up to 300 bp) Length mer GC content 40-60% (preferably 45-55%) T m Make sure the forward primer and the reverse primer do not differ greatly in T m values. Use a special software to determine T m values. OLIGO *1 : Primer3 *2 : Sequence Make sure that overall there are no base sequence biases. Avoid having any GC-rich or AT-rich regions in the sequence (particularly at the 3 end). Avoid having consecutive T/C pairings (polypyrimidine). Avoid having consecutive A/G pairings (polypurine). 3 end sequence Avoid having any GC-rich or AT-rich sequence at the 3 end. It is preferable to have a G or C as the 3 end-base. It is better to avoid a primer design with T as the 3 end-base. Complementation Avoid having any complementary sequences of 3 bases or more within a primer and between primers. Avoid having any complementary sequences of 2 bases or more at the primer's 3' ends. Specificity Verify primer specificity by a BLAST search *3. *1: OLIGO Primer Analysis Software(Molecular Biology Insights) *2: Primer3( *3: 2. When performing real time RT-PCR For reverse transcription reactions by real time RT-PCR, we recommend using PrimeScript RT products [PrimeScript RT reagent Kit (Perfect Real Time) (Cat. #RR037A/B), PrimeScript RT Master Mix (Perfect Real Time) (Cat. #RR036A/B) or PrimeScript RT reagent Kit with gdna Eraser (Perfect Real Time) (Cat. #RR047A/B)] or BluePrint RT Reagent Kit (for Real Time) (Cat. #RR737A). When used in combination with this kit, these products can provide highly reliable results. A. Prepare a PCR mixture by the following procedure. (When using Thermal Cycler Dice Real Time System II) Prepare the following components in volumes slightly more than that needed for the required number of tubes and dispense into aliquots of µl. 12 URL:

13 <Per reaction> Reagent Amount Final conc. SYBR Premix Ex Taq II (2 ) 12.5 µl 1 PCR Forward Primer (10 µm) 1.0 µl 0.4 µm PCR Reverse Primer (10 µm) 1.0 µl 0.4 µm dh2o (sterile distilled water) x µl total µl B. Add µl of the reverse transcription reaction mixture to each of the microtubes containing aliquots of the reaction mixture. Note: Add no more than 2.5 µl of the reverse transcription reaction solution to the PCR mixture. Result: Human B2M mrna was detected with real time RT-PCR. cdna equivalent to 1 pg ng of total RNA was used as the template, with dh 2 O serving as the negative control. Figure 5. Detection of human B2M mrna using real time RT-PCR. URL: 13

14 X. Quality specification 1. Quality test 1.Excellent and stable amplification as well as SYBR Green I detection are demonstrated in a real time PCR with HL60 cdna as template using Thermal Cycler Dice Real Time System (amplification products: 56 and 184 bp). 2. TaKaRa Ex Taq HS A. Definition of activity 1 U is defined as the activity required to incorporate 10 nmol of total nucleotides into acid-insoluble precipitate over 30 minutes at 74 using activated salmon sperm DNA as template/primer. Composition of the reaction mixture for assaying activity 25 mm TAPS buffer (ph9.3, 25 ) 50 mm KCl 2 mm MgCl2 0.1 mm DTT 200 µm each datp, dgtp and dctp 100 µm [ 3 H]-dTTP 0.25 mg/ml Activated salmon sperm DNA B. Purity 1) No change to the DNA electrophoresis pattern is observed after 10 U of this enzyme and 0.6 µg of λ -Hind III degradation product are allowed to react at 74 for 1 hour. 2) No change to the DNA electrophoresis pattern is observed after 10 U of this enzyme and 0.6 µg of supercoiled pbr322 DNA are allowed to react at 74 for 1 hour. 3) No change to the DNA electrophoresis pattern is observed after 10 U of this enzyme and 0.6 µg of λ DNA are allowed to react at 74 for 1 hour. 14 URL:

15 XI. Related products SYBR Premix Ex Taq (Tli RNaseH Plus) (Cat. #RR420A/B) SYBR Premix DimerEraser (Perfect Real Time) (Cat. #RR091A/B) SYBR Premix Ex Taq GC (Perfect Real Time) (Cat. #RR071A/B) BluePrint RT Reagent Kit (for Real Time) (Cat. #RR737A)] PrimeScript RT reagent Kit (Perfect Real Time) (Cat. #RR037A/B)* PrimeScript RT Master Mix (Perfect Real Time) (Cat. #RR036A/B)* PrimeScript RT reagent Kit with gdna Eraser (Perfect Real Time) (Cat. #RR047A/B)* Thermal Cycler Dice Real Time System II (e.g., Cat. #TP900/TP960)** XII. Note * Not available in the United States. ** Not available in the United States or Europe. SYBR is a registered trademark of Molecular Probes Inc., and TaqMan is a trademark of Roche Molecular Systems, Inc. Unless otherwise specified, other trade names are also the trademarks or registered trademarks of various companies. URL: 15

16 NOTICE TO PURCHASER: LIMITED LICENSE [P5] PCR Notice Use of this product is covered by one or more of the following US patents and corresponding patent claims outside the US: 5,079,352, 5,789,224, 5,618,711, 6,127,155, 5,677,152, 5,773,258, 5,407,800, 5,322,770, 5,310,652, 5,994,056, 6,171,785, and claims outside the US corresponding to US Patent No. 4,889,818. The purchase of this product includes a limited, non-transferable immunity from suit under the foregoing patent claims for using only this amount of product for the purchaser's own internal research. No right under any other patent claim (such as instrument or system claims in US Patent No. 6,814,934) and no right to perform commercial services of any kind, including without limitation reporting the results of purchaser's activities for a fee or other commercial consideration, is conveyed expressly, by implication, or by estoppel. This product is for research use only. Diagnostic uses under Roche patents require a separate license from Roche. Further information on purchasing licenses may be obtained by contacting the Director of Licensing, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California 94404, USA. [L11] SYBR Green I This product is covered by the claims of U.S. Patent No. 5,436,134 and 5,658,751 and their foreign counterpart patent claims. Takara PCR products containing SYBR Green I are sold under license from Molecular Probes Inc. only for the usage in Real-time PCR for internal research purpose. These products are not to be used for the purpose such as; providing medical, diagnostic, or any other testing, analysis or screening services or providing clinical information or clinical analysis in return for compensations. [L15] Hot Start PCR Licensed under U.S. Patent No. 5,338,671 and 5,587,287 and corresponding patents in other countries. [L46] SYBR /Melting Curve Analysis The purchase of this product includes a limited, non-transferable license for all fields other than human or veterinary in vitro diagnostics under specific claims of U.S. Patent Nos. 6,174,670, 6,569,627 and 5,871,908, owned by the University of Utah Research Foundation or Evotec Biosystems GmbH and licensed to Idaho Technology, Inc. and Roche Diagnostics GmbH, to use only the enclosed amount of product according to the specified protocols. No right is conveyed, expressly, by implication, or by estoppel, to use any instrument or system under any claim of U.S. Patent Nos. 6,174,670, 6,569,627 and 5,871,908, other than for the amount of product contained herein. [M40] Thermostable RNase H This product is covered by the claims of U.S. Patent No. 7,422,888 and its foreign counterpart patent claims. [M57] LA Technology This product is covered by the claims 6-16 of U.S. Patent No. 5,436,149 and its foreign counterpart patent claims. NOTE : This product is for research use only. It is not intended for use in therapeutic or diagnostic procedures for humans or animals. Also, do not use this product as food, cosmetic, or household item, etc. Takara products may not be resold or transferred, modified for resale or transfer, or used to manufacture commercial products without written approval from TAKARA BIO INC. If you require licenses for other use, please contact us by phone at or from our website at 16 URL: