PCR Protocol for Phusion^® Hot Start Flex DNA Polymerase (M0535)

Overview

The following guidelines are provided to ensure successful PCR using Phusion® Hot Start Flex DNA Polymerase. These guidelines cover routine PCR. Amplification of templates with high GC content, high secondary structure, low template concentrations or long amplicons may require further optimization.

Protocol

1. Reaction Setup: Phusion Hot Start Flex DNA Polymerase is inhibited at room temperature, allowing flexible reaction set up (RT or ice). All components should be mixed and spun down prior to use. Phusion Hot Start Flex DNA Polymerase may be diluted in 1X HF or GC Buffer just prior to use in order to reduce pipetting errors. Please note that protocols with Phusion Hot Start Flex DNA Polymerase may differ from protocols with other standard polymerases. As such, conditions recommended below should be used for optimal performance.
   
   

   COMPONENT	25 μl REACTION	50 μl REACTION	FINAL CONCENTRATION
   Nuclease-free water	to 25 µl	to 50 µl
   5X Phusion HF or GC Buffer	5 µl	10 µl	1X
   10 mM dNTPs	0.5 µl	1 µl	200 µM
   10 µM Forward Primer	1.25 µl	2.5 µl	0.5 µM
   10 µM Reverse Primer	1.25 µl	2.5 µl	0.5 µM
   Template DNA	variable	variable	< 250 ng
   DMSO (optional)	(0.75 µl)	(1.5 µl)	3%
   Phusion Hot Start Flex DNA Polymerase	0.25 µl	0.5 µl	1.0 units/50 µl PCR

   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 to a PCR machine and begin thermocycling. Phusion Hot Start Flex DNA Polymerase does not require a separate activation step. Standard Phusion cycling conditions are recommended.
    

1. Primers:
   Oligonucleotide primers are generally 20–40 nucleotides in length and ideally have a GC content of 40–60%. Computer programs such as Primer3 can be used to design or analyze primers. The final concentration of each primer in a PCR experiment using Phusion Hot Start Flex DNA Polymerase may be 0.2–1 μM, while 0.5 μM is strongly recommended.
    
2. Mg⁺⁺ and additives: 
    
   Mg⁺⁺ is critical to achieve optimal activity with Phusion Hot Start Flex DNA Polymerase. The final Mg⁺⁺ concentration in the 1X Phusion HF and GC Buffer is 1.5 mM.  Excessive Mg⁺⁺ can prevent full denaturation of DNA as well as cause non-specific binding of primers.  The optimal Mg⁺⁺ concentration is affected by dNTP concentration, the template being used and supplements that are added to the reaction.  If chelators (e.g. EDTA) are present, it may be necessary to increase the Mg⁺⁺ concentration.  Mg⁺⁺ can be optimized in 0.5 mM increments using the MgCl2 provided.  
    
   Amplification of difficult targets, such as those with GC-rich sequences or secondary structure, may be improved by the presence of additives such as DMSO (included). A final concentration of 3% DMSO is recommended, although concentration can be optimized in 2% increments. It is important to note that if a high concentration of DMSO is used, the annealing temperature must be lowered as DMSO decreases the primer T_m (2). Phusion Hot Start Flex is also compatible with other additives such as formamide or glycerol
    
3. Deoxynucleotides:
   The final concentration of dNTPs is typically 200 μM of each deoxynucleotide. Phusion Hot Start Flex cannot incorporate dUTP and is not recommended for use with uracil-containing primers or template.
    
4. Phusion Hot Start Flex DNA Polymerase Concentration:
   We generally recommend using Phusion Hot Start Flex DNA Polymerase at a concentration of 20 units/ml (1.0 unit/50 μl reaction). However, the optimal concentration of Phusion Hot Start Flex DNA Polymerase may vary from 10–40 units/ml (0.5–2 units/50 μl reaction) depending on amplicon length and difficulty. Do not exceed 2 units/50 μl reaction, especially for amplicons longer than 5 kb.
    
5. Buffers:
   5X Phusion HF Buffer and 5X Phusion GC Buffer are provided with the enzyme. HF buffer is recommended as the default buffer for high-fidelity amplification. For difficult templates, such as GC-rich templates or those with secondary structure, GC buffer can improve reaction performance. Detergent-free reaction buffers are also available for applications that do not tolerate detergents (e.g. microarray, DHPLC).
    
6. Denaturation:
   Phusion Hot Start Flex DNA Polymerase does not require a separate activation step.
    
   An initial denaturation of 30 seconds at 98°C is sufficient for most amplicons from pure DNA templates. Longer denaturation times can be used (up to 3 minutes) for templates that require it.
    
   During thermocycling, the denaturation step should be kept to a minimum. Typically, a 5–10 second denaturation at 98°C is recommended for most templates.
    
7. Annealing:
   Optimal annealing temperatures for Phusion Hot Start Flex DNA Polymerase tend to be higher than for other PCR polymerases. The  NEB Tm Calculator   should be used to determine the annealing temperature when using Phusion products. Typically, for primers > 20 nt, use a 10–30s annealing step at 3°C above the T_m of the lower T_m primer. For primers < 20 nt, an annealing temperature equivalent to the T_m of the lower primer should be used. A temperature gradient can also be used to optimize the annealing temperature for each primer pair. For two-step cycling, the gradient can be set as high as the extension temperature.
    
   For high T_m primer pairs, two-step cycling without a separate annealing step can be used.
    
8. Extension:
   The recommended extension temperature is 72°C. Extension times are dependent on amplicon length and complexity. Generally, an extension time of 15 seconds per kb can be used. For complex amplicons, such as genomic DNA, an extension time of 30 seconds per kb is recommended. Extension time can be increased to 40 seconds per kb for cDNA templates, if necessary.
    
9. Cycle number:
   Generally, 25–35 cycles yield sufficient product.
    
10. 2-step PCR:
    When primers with annealing temperatures ≥ 72°C are used, a 2-step thermocycling protocol is recommended.
     
    Thermocycling Conditions for a Routine 2-Step PCR:

    STEP	TEMP	TIME
    Initial Denaturation	98°C	30 Seconds
    25-35 Cycles	98°C  72°C	5-10 Seconds 15-30 Seconds/kb
    Final extension	72°C	5-10 minutes
    Hold	4-10°C

     
11. PCR product:
    The PCR products generated using Phusion Hot Start Flex DNA Polymerase have blunt ends. If cloning is the next step, then blunt-end cloning is recommended. If T/A-cloning is preferred, the DNA should be purified prior to A-addition, as Phusion Hot Start Flex DNA Polymerase will degrade any overhangs generated.
     
    Addition of an untemplated -dA can be done with Taq DNA Polymerase (NEB #M0267 ) or Klenow exo^– (NEB #M0212 ).