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  • Protocol for Taq 5X Master Mix (M0285)

    Overview

    PCR 
    The Polymerase Chain Reaction (PCR) is a powerful and sensitive technique for DNA amplification (1). Taq DNA Polymerase is an enzyme widely used in PCR (2). The following guidelines are provided to ensure successful PCR using New England Biolabs’ Taq 5X Master Mix. These guidelines cover routine amplification reactions. Amplification of templates with high GC content, high secondary structure, low template concentrations, or amplicons greater than 5 kb may require further optimization.

    Protocol

    Reaction setup:

    We recommend assembling all reaction components on ice and quickly transferring the reactions to a thermocycler preheated to the denaturation temperature (95°C). 

    Component 25 µl Reaction 50 µl Reaction Final Concentration
    10 µM Forward Primer 0.5 µl 1 µl 0.2 µM (0.05–1 µM)
    10 µM Reverse Primer 0.5 µl 1 µl 0.2 µM (0.05–1 µM)
    Template DNA variable variable <1,000 ng
    Taq 5X Master Mix 5 µl 10 µl 1X
    Nuclease-free water to 25 µl to 50 µl  
    Notes: Gently mix the reaction. Collect all liquid to the bottom of the tube by a quick spin if necessary. Overlay the sample with mineral oil if using a PCR machine without a heated lid.

    Transfer PCR tubes from ice to a PCR machine with the block preheated to 95°C and begin thermocycling: 

    Thermocycling conditions for a routine PCR:


    STEP
    TEMP
    TIME
    Initial Denaturation
    95°C
    30 seconds
    30 Cycles 95°C
    45-68°C
    68°C
    15-30 seconds
    15-60 seconds
    1 minute/kb
    Final Extension 68°C
    5 minutes
    Hold 4-10°C
     

    General Guidelines
    1. Template: 

      Use of high quality, purified DNA templates greatly enhances the success of PCR. Recommended amounts of DNA template for a 50 μl reaction are as follows: 
      DNA Amount
      genomic 1 ng–1 μg
      plasmid or viral 1 pg–1 ng
    2. Primers: 

      Oligonucleotide primers are generally 20–40 nucleotides in length and ideally have a GC content of 40–60%. Computer programs such as Primer3 (http://frodo.wi.mit.edu/primer3) can be used to design or analyze primers. The final concentration of each primer in a reaction may be 0.05–1 μM, typically 0.1–0.5 μM.

    3. Mg++ and additives: 

      Mg++ concentration of 1.5–2.0 mM is optimal for most PCR products generated with Taq DNA Polymerase. The final Mg++ concentration in 1X Taq Master Mix is 1.5 mM. This supports satisfactory amplification of most amplicons. However, Mg++ can be further optimized in 0.5 or 1.0 mM increments using MgCl2

      Amplification of some difficult targets, like GC-rich sequences, may be improved with additives, such as DMSO (3) or formamide (4).

    4. Denaturation: 

      An initial denaturation of 30 seconds at 95°C is sufficient for most amplicons from pure DNA templates. For difficult templates such as GC-rich sequences, a longer denaturation of 2–4 minutes at 95°C is recommended prior to PCR cycling to fully denature the template. With colony PCR, an initial 5 minute denaturation at 95°C is recommended. 

      During thermocycling a 15–30 second denaturation at 95°C is recommended.

    5. Annealing: 

      The annealing step is typically 15–60 seconds. Annealing temperature is based on the Tm of the primer pair and is typically 45–68°C. Annealing temperatures can be optimized by doing a temperature gradient PCR starting 5°C below the calculated Tm

      When primers with annealing temperatures above 65°C are used, a 2-step PCR protocol is possible (see #8).

    6. Extension: 

      The recommended extension temperature is 68°C. Extension times are generally 1 minute per kb. A final extension of 5 minutes at 68°C is recommended. 

    7. Cycle number: 

      Generally, 25–35 cycles yields sufficient product. Up to 45 cycles may be required to detect low-copy-number targets. 

    8. 2-step PCR: 
      When primers with annealing temperatures above 65°C are used, a 2-step thermocycling protocol is possible. 

      Thermocycling conditions for a routine 2-step PCR:
      STEP
      TEMP
      TIME
      Initial Denaturation 95°C 30 seconds
      30 Cycles 95°C
      65-68°C
      15-30 seconds
      1 minute/kb
      Final Extension 65-68°C 5 minutes
      Hold 4-10°C
    9. PCR product: 

      The PCR products generated using Taq DNA Polymerase contain dA overhangs at the 3´–end; therefore the PCR products can be ligated to dT/dU-overhang vectors.

    References:
    1.  Saiki R.K. et al. (1985). Science. 230, 1350-1354.
    2.  Powell, L.M. et al. (1987). Cell. 50, 831-840.
    3.  Sun, Y., Hegamyer, G. and Colburn, N. (1993). Biotechniques. 15, 372-374.
    4.  Sarkar, G., Kapelner, S. and Sommer, S.S. (1990). Nucleic Acids Res.. 18, 7465.