Agilent Pfu DNA Polymerase 600135 Chain Reaction Instruction Manual PDF

Pfu DNA Polymerase

Instruction Manual

Catalog #600135, #600136, and #600140 (Native Pfu DNA Polymerase) and #600153, #600154, #600159, and #600160 (Cloned Pfu DNA Polymerase)

Revision G0

Laboratory Reagent. 600135-12

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Pfu DNA Polymerase

CONTENTS Materials Provided .............................................................................................................................. 1 Storage Conditions .............................................................................................................................. 1 Notices to Purchaser ........................................................................................................................... 1 Introduction ......................................................................................................................................... 2 Critical Optimization Parameters for Pfu DNA Polymerase-Based PCR ..................................... 2

Extension Time ...................................................................................................................... 2 Enzyme Concentration .......................................................................................................... 2 Reaction Buffer ..................................................................................................................... 3 PrimerTemplate Purity and Concentration .......................................................................... 4 Primer Design ........................................................................................................................ 4

Additional Optimization Parameters for Pfu DNA Polymerase-Based PCR ................................ 5 PCR Cycling Parameters ....................................................................................................... 5 Order of Addition of Reaction Mixture Components ............................................................ 5 Deoxynucleoside Triphosphates ............................................................................................ 5 Salt Concentrations ................................................................................................................ 6 Adjuncts and Cosolvents ....................................................................................................... 6

Application Notes ................................................................................................................................ 7 Long PCR .............................................................................................................................. 7 Thermostability ..................................................................................................................... 7 Modified Nucleotide Incorporation ....................................................................................... 7 Terminal Transferase Activity ............................................................................................... 7 Reverse Transcriptase Activity .............................................................................................. 8

PCR Protocol Using Pfu DNA Polymerase ....................................................................................... 9 Troubleshooting ................................................................................................................................ 11 Preparation of Media and Reagents ................................................................................................ 12 References .......................................................................................................................................... 12 MSDS Information ............................................................................................................................ 13

Pfu DNA Polymerase 1

Pfu DNA Polymerase

MATERIALS PROVIDED

Native Pfu DNA Polymerase

Materials provided

Quantity

Catalog #600135 Catalog #600136 Catalog #600140

Native Pfu DNA polymerase (2.5 U/l) 100 Ua 500 Ub 1000 Uc

Native Plus 10 Pfu buffer 1 ml 2 1 ml 4 1 ml a Sufficient native Pfu DNA polymerase is provided for up to 40 100-l reactions. b Sufficient native Pfu DNA polymerase is provided for up to 200 100-l reactions. c Sufficient native Pfu DNA polymerase is provided for up to 400 100-l reactions.

Cloned Pfu DNA Polymerase

Materials provided

Quantity

Catalog #600153

Catalog #600154

Catalog #600159

Catalog #600160

Cloned Pfu DNA polymerase (2.5 U/l) 100 Ua 500 Ub 1000 Uc 5000 Ud

10 Cloned Pfu buffere 1 ml 2 1 ml 4 1 ml 20 1 ml a Sufficient cloned Pfu DNA polymerase is provided for up to 40 100-l reactions. b Sufficient cloned Pfu DNA polymerase is provided for up to 200 100-l reactions. c Sufficient cloned Pfu DNA polymerase is provided for up to 400 100-l reactions. d Sufficient cloned Pfu DNA polymerase is provided for up to 2000 100-l reactions. e See Preparation of Media and Reagents.

STORAGE CONDITIONS

All components: 20C

NOTICES TO PURCHASER

Limited Label License for Native and Cloned Pfu DNA Polymerase Products Purchase of this product conveys to the purchaser the non-transferable right to use the product for research use only. No rights are granted to the purchaser hereunder to sell, modify for resale or otherwise transfer this product, either alone or as a component of another product, to any third party. Agilent reserves all other rights, and this product may not be used in any manner other than as provided herein.

Revision G0 Agilent Technologies, Inc. 2015, 2020.

2 Pfu DNA Polymerase

INTRODUCTION Pfu DNA polymerase, a proofreading DNA polymerase isolated from Pyrococcus furiosus, is an ideal choice for a variety of techniques requiring high-fidelity DNA synthesis by the polymerase chain reaction (PCR).13 These applications include cloning, gene expression, and site-directed mutagenesis. Successful PCR using Pfu DNA polymerase is readily performed requiring only slight modifications from PCR protocols optimized with Taq DNA polymerase. Various PCR parameters that are important in increasing the yield and specificity of Pfu DNA polymerase- based PCR amplification reactions are described in this instruction manual.

CRITICAL OPTIMIZATION PARAMETERS FOR Pfu DNA POLYMERASE- BASED PCR

All PCR amplification reactions, whether performed using Taq or Pfu DNA polymerase, require optimization to achieve the highest product yield and specificity. Critical optimization parameters for successful PCR using Pfu DNA polymerase are outlined in the following sections and include the use of an extension time that is adequate for full-length DNA synthesis, sufficient enzyme concentration, optimization of the reaction buffer, adequate primertemplate purity and concentration, and optimal primer design.

Extension Time Extension time is the most critical parameter affecting the yield of PCR product obtained using Pfu DNA polymerase. For Taq DNA polymerase- based PCR amplifications, an extension time of 0.5-1.0 minute/kb of template amplified is usually sufficient for maximum synthesis of a PCR target. In contrast, Pfu DNA polymerase-based PCR amplifications require a minimum extension time of 1-2 minutes/kb of amplified template to achieve similar target synthesis.4

Enzyme Concentration The concentration of Pfu DNA polymerase required for optimal PCR product yield and specificity depends on the individual target system to be amplified. Successful amplification can usually be achieved using 2.55.0 U of enzyme/100-l reaction for PCR targets that are <2 kb. Further optimization will be required for targets greater than 2 kb.

Pfu DNA Polymerase 3

TABLE I

Fidelity Comparison of Thermostable DNA Polymerases Using a lacIOZ-Based Fidelity Assaya

Thermostable DNA polymerase

Error rateb Percentage (%) of mutated PCR productsc

Pfu DNA polymerase 1.3 106 2.6

Taq DNA polymerase 8.0 106 16.0

VentR DNA polymerase 2.8 106 5.6

Deep VentR DNA polymerase 2.7 106 5.4 a Fidelity is measured using a PCR-based forward mutation assay based on the lacI target

gene.5 b The error rate equals mutation frequency per base pair per duplication. c The percentage of mutated PCR products after amplification of a 1-kb target sequence

for 20 effective cycles.

Reaction Buffer In Pfu DNA polymerase-based PCR, the reaction buffers for native and cloned Pfu DNA polymerases are formulated for optimal PCR yield and fidelity.6 Use the 10 reaction buffer provided with each polymerase for all PCR applications. If alterations in the Pfu reaction buffers are made, significant increases in the error rate of Pfu DNA polymerase can be avoided by maintaining the Mg2+ concentration above 1.5 mM, the total dNTP concentration at or below 1 mM, and the pH of Tris-based buffers above pH 8.0 when measured at 25C. Deoxynucleoside triphosphate (dNTP) concentrations of 100250 M each dNTP generally result in the optimal balance of product yield (greatest at high dNTP concentrations) versus specificity and fidelity (highest at low dNTP concentration).7

4 Pfu DNA Polymerase

PrimerTemplate Purity and Concentration The most successful PCR results are achieved when the amplification reaction is performed using purified primers and templates that are essentially free of extraneous salts. Gel-purified primers, generally >18 nucleotides in length, are strongly recommended for use in Pfu DNA polymerase-based PCR. Additionally, an adequate concentration of primers and template should be used to ensure a good yield of the desired PCR products. When DNA of known concentration is available, amounts of 50200 ng of DNA template/100-l reaction are typically used for amplifying single-copy chromosomal targets. Amplifying a single-copy target from complex genomic DNA is generally more difficult than amplifying a fragment from a plasmid or phage. Less DNA template can be used for amplifying lambda or plasmid PCR targets or for amplifying multicopy chromosomal genes (typically 10100 ng).7 The mutation frequency can be reduced by limiting the number of PCR cycles; however, a corresponding increase in DNA template concentration is required to achieve comparable yields of PCR product. We suggest using primers at a final concentration of 0.10.5 M, which is equivalent to ~100250 ng of an 18- to 25-mer oligonucleotide primer in a 100-l reaction volume. Relatively high concentration of primers is typically required due to the fact that proofreading DNA polymerases such as Pfu DNA polymerase exhibit 3- to 5-exonuclease activity, which may contribute to a certain level of primer degradation. The use of primers with a phosphorothioate bond at the 3-terminal internucleotide linkage reportedly minimizes primer degradation.9

Primer Design Primer pairs that exhibit similar melting temperatures and are completely complementary to the template are recommended. Depending on the primer design and the desired specificity of the PCR amplification reaction, melting temperatures between 55 and 80C generally yield the best results.7 The following formula10 is commonly used for estimating the melting temperature (Tm) of the primers:

T N N N Nm A T G C( C) 2( ) 4( ) where N equals the number of primer adenine (A), thymidine (T), guanidine (G), or cytosine (C) bases. Several other articles present additional equations for estimating the melting temperature of the primers.11,12 Finally, care must be taken when using degenerate primers. Degenerate primers should be designed with the least degeneracy at the 3 end. Optimization of degenerate primer concentration is necessary.

Note Because of the unique composistion of the Pfu buffer, the actual primer Tm may be 35C lower than that estimated by this forumla.

Pfu DNA Polymerase 5

ADDITIONAL OPTIMIZATION PARAMETERS FOR Pfu DNA POLYMERASE-BASED PCR

PCR Cycling Parameters Standard PCR amplification reactions typically require 2530 cycles to obtain a high yield of PCR product. Because high fidelity is a concern for certain PCR applications such as expression cloning, We suggest using a minimum number of cycles for Pfu DNA polymerase-based PCR to ensure the lowest number of errors. Thermal cycling parameters should be chosen carefully to ensure (1) the shortest denaturation times to avoid enzyme inactivation and/or template damage, (2) adequate extension times to achieve full-length target synthesis, and (3) the use of annealing temperatures near the primer melting temperature to improve specificity of the desired PCR product. When performing PCR on a new target system, we suggest using an annealing temperature 510C below the lowest primer melting temperature. For best results, PCR primers should be designed with similar melting temperatures ranging from 55 to 80C. The use of primers with melting temperatures within this range reduces false priming and ensures complete denaturation of unextended primers at 9495C (see also PrimerTemplate Purity and Concentration and Primer Design).

Order of Addition of Reaction Mixture Components Because Pfu DNA polymerase exhibits 3- to 5-exonuclease activity that enables the polymerase to proofread nucleotide misincorporation errors, it is critical that Pfu DNA polymerase is the last component added to the PCR mixture (i.e., after the dNTPs). In the absence of dNTPs, the 3- to 5- exonuclease activity of proofreading DNA polymerases may degrade primers. When primers and nucleotides are present in the reaction mixture at recommended levels (i.e., primer concentrations of 0.10.5 M and nucleotide concentrations of 100-250 M), primer degradation is minimal.

Deoxynucleoside Triphosphates For Pfu DNA polymerase-based PCR, we recommend using a dNTP concentration range of 100250 M each dNTP (0.41.0 mM total) in order to achieve the optimal balance between yield, specificity, and fidelity. Deoxynucleoside triphosphate concentrations of 100250 M each dNTP generally result in the optimal balance of product yield (greatest at high dNTP concentrations) versus specificity and fidelity (highest at low dNTP concentration).7 The use of a balanced pool of dNTPs (equimolar amounts of each dNTP) ensures the lowest rate of misincorporation errors.

6 Pfu DNA Polymerase

Salt Concentrations

Magnesium Concentration Magnesium chloride concentration affects primer annealing and template denaturation, as well as enzyme activity and fidelity. Generally, excess Mg2+ concentration results in accumulation of nonspecific amplification products, whereas insufficient Mg2+ concentration results in reduced yield of the desired PCR product.13 PCR amplification reactions should contain free Mg2+ in excess of the total dNTP concentration. For Pfu DNA polymerase- based PCR, yield is optimal when the total Mg2+ concentration is ~2 mM in a standard reaction mixture, and ~3 mM for amplification of cDNA. A 2 mM total Mg2+ concentration is present in the final 1 dilution of the 10 reaction buffer provided. For the amplification of cDNA, Mg2+ should be added to the PCR reaction to a final concentration of 3 mM.7

Adjuncts and Cosolvents The adjuncts or cosolvents listed in the following table may be advantageous with respect to yield when used in the PCR buffer. Fidelity may or may not be affected by the presence of these adjuncts or cosolvents.

Adjunct or cosolvent Optimal PCR final concentration

Bovine serum albumin (BSA) 10100 g/ml

Formamide 1.2510%

Dimethylsulfoxide (DMSO) 110%

Glycerol 520%

Ammonium sulfate [(NH4)2SO4] 1530 mM

Perfect Match PCR enhancer 1 U/100-l reaction (genomic DNA template)

0.011 U/100-l reaction (plasmid DNA template)

Bovine Serum Albumin Bovine serum albumin is a nonspecific enzyme stabilizer that also binds certain PCR inhibitors.14

Formamide Formamide facilitates certain primertemplate annealing reactions and also lowers the denaturing temperature of melt-resistant DNA.15

Dimethylsulfoxide and Glycerol Cosolvents, such as DMSO and glycerol, improve the denaturation of GC-rich DNA and help overcome the difficulties of polymerase extension through secondary structures. Studies indicate that the presence of 110% DMSO in PCR may be essential for the amplification of the retinoblastoma gene16 and may also enhance amplification of Herpes simplex virus (HSV) sequences. Glycerol is known to improve the yield of amplification products and also serves as an enzyme stabilizer.17

Pfu DNA Polymerase 7

Ammonium Sulfate Ammonium sulfate increases the ionic strength of the reaction mixture, which alters the denaturing and annealing temperatures of DNA, as well as enzyme activity.

Perfect Match PCR Enhancer Perfect Match PCR enhancer improves the specificity of PCR products. This adjunct performs these functions by destabilizing mismatched primer template complexes and helps to remove secondary structures that could impede normal extension.18

APPLICATION NOTES

Long PCR Native Pfu DNA polymerase successfully synthesizes PCR targets up to 12- kb from either plasmid or genomic templates.19 In long PCR amplification reactions, product yields are greatest when the reaction is performed using Agilents Native Pfu DNA polymerase in combination with the Native Plus 10 Pfu buffer.

Thermostability Pfu DNA polymerase is a highly thermostable enzyme, retaining 94-99% of its polymerase activity after 1 hour at 95C. Unlike Taq DNA polymerase, denaturing temperatures up to 98C can be used successfully with Pfu DNA polymerase to amplify GC-rich regions.19,20

Modified Nucleotide Incorporation Pfu DNA polymerase successfully incorporates the following modified nucleotides: -thionucleotides, 7-deaza-deoxyguanosine triphosphate (7- deaza-dGTP), and fluoresceinated and biotinylated nucleotides. Efficient incorporation of modified nucleotides may require optimization of the analog concentration. Exo Pfu DNA polymerase incorporates these modified nucleotides more efficiently than the Exo+ version of the DNA polymerase due to the lack of an associated proofreading activity.

Terminal Transferase Activity Studies demonstrate that thermostable DNA polymerases with the exception of Pfu DNA polymerase exhibit terminal deoxy-nucleotidyltransferase (TdT) activity, which is characterized by the addition of nontemplate- directed nucleotide(s) at the 3 end of PCR-generated fragments.21,22 Pfu DNA polymerase is devoid of TdT activity and generates blunt-ended PCR products exclusively. Therefore, this is the enzyme of choice for use with the PCR-Script Amp SK(+) cloning kit23 and the PCR-Script Cam SK(+) cloning kit.24 Alternatively, Pfu DNA polymerase can be used to remove 3 overhangs (polishing) or to fill-in 5 overhangs with greater efficiencies than either Klenow polymerase or T4 DNA polymerase.25,26

8 Pfu DNA Polymerase

Reverse Transcriptase Activity Pfu DNA polymerase lacks detectable reverse transcriptase activity.

Pfu DNA Polymerase 9

PCR PROTOCOL USING Pfu DNA POLYMERASE

1. Prepare a reaction mixture for the appropriate number of samples to be amplified. Add the components in order while mixing gently. Table II provides an example of a reaction mixture for the amplification of a typical single-copy chromosomal target. The recipes listed in Table II are for one reaction and must be adjusted for multiple samples. The final volume of each sample reaction is 100 l.

Note The volumes of each component in the reaction mixture may also be decreased proportionally to a 50-l final volume.

2. Immediately before thermal cycling, aliquot 100 l of the reaction mixture into the appropriate number of reaction tubes.

3. Perform PCR using optimized cycling conditions. Suggested cycling parameters are indicated in Table III.

4. Analyze the PCR amplification products on a 0.71.0% (w/v) agarose gel.

TABLE II

Reaction Mixture for a Typical Single-Copy Chromosomal Locus PCR Amplification

Component Amount per reaction

Distilled water (dH2O) 81.2 l

10 buffera 10.0 l

dNTPs (25 mM each NTP) 0.8 l

DNA template (100 ng/l) 1.0 lb

Primer #1 (100 ng/l) 2.5 lc

Primer #2 (100 ng/l) 2.5 lc

Native or cloned Pfu DNA polymerase (2.5 U/l) 2.0 l (5.0 U)d

Total reaction volume 100 l a The 10 buffer provides a final 1 Mg2+ concentration of 2 mM. To amplify cDNA, Mg2+ may need to be added to

a final 1 concentration of 3 mM.

b The amount of DNA template required varies depending on the type of DNA being amplified. Generally 50200 ng of genomic DNA template is recommended; however, less DNA template (typically 1100 ng) can be used for amplification of lambda or plasmid PCR targets or for amplification of multicopy chromosomal genes.

c Primer concentrations between 0.1 and 0.5 M are recommended (generally 100250 ng for typical 18- to 25-mer oligonucleotide primers in a 100-l reaction volume).

d The amount of Pfu DNA polymerase varies depending on the length of the template to be amplified. A typical starting point is 5.0 U. Successful amplification can usually be achieved using 2.55.0 U of enzyme/100-l reaction for PCR targets that are <2 kb. Further optimization will be required for targets greater than 2 kb.

10 Pfu DNA Polymerase

TABLE III

Suggested Cycling Parameters for PCR Using Pfu DNA Polymerase

Segment Number of cycles Temperature Duration

1 1 9498Ca 45 seconds

2 2530 9498C

Primer Tm 5Cb

72C

45 seconds

45 seconds

12 minutes/kb of PCR target

3 1 72C 10 minutes a Denaturing temperatures above 95C are recommended only for GC-rich templates. b The annealing temperature may be lowered further if necessary to obtain optimal results. Typically annealing

temperatures will range between 55 and 72C.9

Pfu DNA Polymerase 11

TROUBLESHOOTING Observation Suggestion(s)

No product or low yield Allow an extension time of at least 1-2 minutes/kb of PCR target

Optimize annealing temperature by lowering it in 5C increments

Ensure that the appropriate buffer is used (i.e., use Native Plus 10 Pfu buffer with native Pfu DNA polymerase and use 10 cloned Pfu buffer with cloned Pfu DNA polymerase)

Add Pfu DNA polymerase last to the reaction mixture to minimize any potential primer degradation

To minimize the effects of high-GC content or secondary structure use higher denaturing temperatures (9498C)

To minimize the effects of high-GC content or secondary structure, use cosolvents such as DMSO in a 110% (v/v) final concentration or glycerol in a 520% (v/v) final concentration (see Dimethylsulfoxide and Glycerol)

Ensure that primer concentration is not too low. Use the recommended primer concentrations between 0.1 and 0.5 M (generally 100250 ng for typical 18- to 25- mer oligonucleotide primers in a 100-l reaction volume)

Ensure that primers used are of high quality

Optimize primers with respect to melting temperature, purity, GC content, and length

Consider using adjuncts to optimize PCR [e.g., use 12 U of Perfect Match PCR enhancer or a low concentration (15%) of formamide]

Ensure the ionic strength of the reaction mix is correct. Remove extraneous salts from the PCR primers and DNA preparations

Optimize denaturation time. Denaturation times of 3060 seconds at 9495C are usually sufficient while longer denaturation times may damage the DNA template; use the shortest denaturation time compatible with successful PCR on the thermal cycler

Increase the amount of Pfu DNA polymerase

Ensure that template used is intact and of high purity. Use template at an adequate concentration (see PrimerTemplate Purity and Concentration and Primer Design)

Titrate the amount of DNA template to ensure template concentration is not too high

See the Adjuncts and Cosolvents section for information about optimal adjuncts and solvents

Multiple bands Optimize primer annealing temperature by increasing the annealing temperature in 5C increments and/or use a hot start27,28

Check for nonspecific primer-template annealing. Use Perfect Match PCR enhancer to improve PCR product specificity

Artifactual smears Decrease the amount of Pfu DNA polymerase

Ensure that extension time is not too long.

12 Pfu DNA Polymerase

PREPARATION OF MEDIA AND REAGENTS 10 Cloned Pfu Buffer

200 mM Tris-HCl (pH 8.8) 20 mM MgSO4 100 mM KCl 100 mM (NH4) 2SO4 1% Triton X-100 1 mg/ml nuclease-free BSA

REFERENCES 1. Cha, R. S. and Tilly, W. G. (1995). In PCR Primer,C. W. Dieffenbach and G. S.

Dveksler (Eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.

2. Lundberg, K. S., Shoemaker, D. D., Adams, M. W., Short, J. M., Sorge, J. A. et al. (1991) Gene 108(1):1-6.

3. Flaman, J. M., Frebourg, T., Moreau, V., Charbonnier, F., Martin, C. et al. (1994) Nucleic Acids Res 22(15):3259-60.

4. Nielson, K. B., Costa, G. L. and Braman, J. (1996) Strategies 9(1):2425. 5. Cline, J., Braman, J. C. and Hogrefe, H. H. (1996) Nucleic Acids Res

24(18):3546-51. 6. Cline, J., Braman, J. and Kretz, K. (1995) Strategies 8(1):2425. 7. Innis, M. A., Gelfand, D. H., Sninsky, J. J. and White, T. J. (1990). PCR

Protocols: A Guide to Methods and Applications. Academic Press, New York. 8. Schoettlin, W., Nielson, K. and Mathur, E. (1993) Strategies 6(2):43-44. 9. Skerra, A. (1992) Nucleic Acids Res 20(14):3551-4. 10. Thein, S. L. and Wallace, R. B. (1986). Human Genetic Diseases: A Practical

Approach. IRL Press, Herndon, Virginia. 11. Rychlik, W., Spencer, W. J. and Rhoads, R. E. (1990) Nucleic Acids Res

18(21):6409-12. 12. Wu, D. Y., Ugozzoli, L., Pal, B. K., Qian, J. and Wallace, R. B. (1991) DNA Cell

Biol 10(3):233-8. 13. Saiki, R. (1989). Chapter 1. In PCR Technology: Principles and Applications for

DNA Amplification,H. A. Erlich (Ed.). Stockton Press, New York. 14. Paabo, S., Gifford, J. A. and Wilson, A. C. (1988) Nucleic Acids Res 16(20):9775-

87. 15. Sarkar, G., Kapelner, S. and Sommer, S. S. (1990) Nucleic Acids Res

18(24):7465. 16. Hung, T., Mak, K. and Fong, K. (1990) Nucleic Acids Res 18(16):4953. 17. Smith, K. T., Long, C. M., Bowman, B. and Manos, M. M. (1990) Amplifications

5:16-17. 18. Nielsen, K. and Mather, E. (1990) Strategies 3(2):17-22. 19. Nielson, K. B., Braman, J. and Kretz, K. (1995) Strategies 8(1):26. 20. Chong, S. S., Eichler, E. E., Nelson, D. L. and Hughes, M. R. (1994) Am J Med

Genet 51(4):522-6. 21. Hu, G. (1993) DNA Cell Biol 12(8):763-770. 22. Costa, G. L., Grafsky, A. and Weiner, M. P. (1994) PCR Methods Appl 3(6):338-

45. 23. Bauer, J. C., Deely, D., Braman, J., Viola, J. and Weiner, M. P. (1992) Strategies

5(3):62-64. 24. Costa, G. L., Sanchez, T. and Weiner, M. P. (1994) Strategies 7(2):52. 25. Costa, G. L. and Weiner, M. P. (1994) Nucleic Acids Res 22(12):2423.

Pfu DNA Polymerase 13

26. Eliason, E. and Detrick, J. (1995) Strategies<