Home Protocols Protocol for LongAmp™ Hot Start Taq 2X Master Mix

Protocol for LongAmp™ Hot Start Taq 2X Master Mix

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). LongAmp Hot Start Taq DNA Polymerase allows for greater PCR sensitivity and permits room temperature PCR set-up. The following guidelines are provided to ensure successful PCR using New England Biolabs’ LongAmp Hot Start Taq 2X Master Mix. These guidelines cover routine PCR. Amplification of templates with high GC content, high secondary structure or low template concentrations may require further optimization.

Protocol

Reaction setup:

Due to the hot-start nature of the enzyme, reactions can be assembled on the bench at room temperature and transferred to a thermocycler. No separate activation step is required.

COMPONENT 25 µl REACTION  50 µl REACTION FINAL CONCENTRATION
LongAmp Hot Start
Taq 2X Master Mix		 12.5 µl 25 µl 1X
10 µM Forward Primer 1 µl 2 µl 0.4 µM (0.05–1 µM)
10 µM Reverse Primer 1 µl 2 µl 0.4 µM (0.05–1 µM)
Template DNA variable variable <1,000 ng
Nuclease-free water to 25 µl to 50 µl

Notes: Gently mix the reaction. Avoid pipetting samples containing target DNA when amplicons above 20 kb are desired. 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 to a PCR machine and begin thermocycling:

Thermocycling conditions for a routine PCR:

STEP TEMP TIME
Initial Denaturation
94°C
30 seconds
30 Cycles 94°C
45-65°C
65°C
10-30 seconds
15-60 seconds
50 seconds per kb
Final Extension 65°C
10 minutes
Hold 4-10°C
 


General Guidelines

  1. Template:

    The quality of the DNA template is essential for long-range PCR amplification. Recommended amounts of DNA template for a 50 μl reaction are as follows:
    DNA UP TO 15 kb ABOVE 15 kb
    Genomic 1 ng–500 ng 10 ng–1 µg
    Plasmid or Viral 1 pg–10 ng 10 pg–10 ng
    Successful amplification above 20 kb largely depends on the quality of DNA templates and the primer sequences.

  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 (https://bioinfo.ut.ee/primer3) can be used to design or analyze primers. For amplicons larger than 20 kb, it is desirable to have primers with GC content above 50%, matched Tm above 60°C and at least 24 nucleotides in length. The final concentration of each primer in a reaction may be 0.05–1 μM, typically 0.1–0.5 μM.

  3. Mg++, Deoxynucleotides and Additives:

    At a 1X concentration, LongAmp Hot Start Taq 2X Master Mix contains 2 mM MgSO4 and 300 μM of each dNTP in the final reaction. This supports satisfactory amplification of most amplicons. However, Mg++ can be further optimized in 0.5 or 1.0 mM increments using MgSO4 (NEB# B1003).

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

  4. Denaturation:

    LongAmp Hot Start Taq DNA Polymerase does not require a separate activation step.

    An initial denaturation of 30 seconds at 94°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 94°C is recommended prior to PCR cycling to fully denature the template. With colony PCR, an initial 5 minute denaturation at 94°C is recommended.

    During thermocycling, a 10-30 second denaturation at 94 °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 45–65°C. Annealing temperatures can be optimized by doing a temperature gradient PCR starting 5°C below the calculated Tm. We recommended using NEB's Tm Calculator to determine appropriate annealing temperature for PCR.

    When primers with annealing temperatures above 60°C are used, a 2-step PCR protocol is possible (see #8).

  6. Extension:

    The recommended extension temperature is 65°C. Extension times are generally 50 seconds per kb. A final extension of 10 minutes at 65°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 60°C are used, a 2-step thermocycling protocol is possible.

    Thermocycling conditions for a routine 2-step PCR:

    STEP TEMP TIME
    Initial Denaturation 94°C 30 seconds
    30 Cycles 94°C
    60-65°C     		10-30 seconds
    50 seconds per kb
    Final Extension 60-65°C 10 minutes
    Hold 4-10°C
  9. PCR product:

    The majority of the PCR products generated using LongAmp Hot Start Taq 2X Master Mix contain dA overhangs at the 3´-end. Therefore, the PCR products can be ligated to the 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.