LongAmp™ Taq DNA Polymerase Guidelines

Protocol

1. Reaction setup:
   We recommend assembling all reaction components on ice and quickly transferring the reactions to a thermocycler preheated to the denaturation temperature (94-95°C).
2. Template: 
   The quality of the DNA template is essential for long-range PCR amplification. Recommended amounts of DNA template for a 50 μl reaction is as follows:

   	up to 15 kb	above 15 kb
   genomic DNA	1 ng - 500 ng	10 ng - 1 µg
   plasmid or viral DNA	1 pg - 1 ng	10 pg - 10 ng

   Successful amplification above 20 kb largely depends on the quality of DNA templates and the primer sequences.
3. Primer:
   Primers are generally 20–40 nucleotides in length and ideally have a GC content of 40-60% (2). Computer programs such as Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) 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 primers at least 24 nucleotides in length. The final concentration of each primer in a typical PCR reaction is 0.05-1 μM, ideally 0.2-0.5 μM.
4. Mg⁺⁺ and additives:
   The final Mg⁺⁺ concentration in the 1X reaction buffer is 2 mM. This gives satisfactory amplification of most amplicons. However, Mg⁺⁺ can be further optimized in 0.2 mM increments using MgSO₄.
   For some difficult targets such as GC-rich sequences, additives such as DMSO (3) and formamide (4) may be included to improve amplification.
5. Denaturation:
   An initial denaturation of 30 seconds at 94-95°C is sufficient for most amplicons from pure DNA templates. For difficult templates such as GC-rich sequences, longer denaturation of 2-4 minutes at 94-95°C is recommended prior to PCR cycling to fully denature the template. With colony PCR, an initial 5 minute denaturation at 94-95°C is recommended. Subsequent denaturation can be done between 10-30 seconds.
6. Annealing:
   The annealing step is typically 10-60 seconds. Annealing temperature can be optimized by doing a temperature gradient PCR starting 5°C below the calculated Tm.
7. Extension:
   Extensions are recommended to be carried out at 65°C. For amplicons below 20 kb, extension can be carried out from 60-68°C. A final extension of 10 minutes at 65°C is recommended.
8. 2-step PCR
   When primers with annealing temperature above 60°C are used, a 2-step PCR protocol is possible.
   Initial denaturation: 
     94-95°C 30 seconds
   25-45 cycles: 
     94-95°C 10 seconds
     60-65°C 50 seconds per kb
   Final extension: 
     60-65°C 10 minutes
   Final soak: 
     4-10°C
9. Cycle number:
   Generally, 25-35 cycles give optimal amplification. Up to 45 cycles may be required to detect low-copy targets. 

References:

1. Barnes, W.M. (1994) Proc. Natl. Acad. Sci., 91, 2216–2220.
2. Foord, O.S. and Rose, E.A. (1994) PCR Methods Appl., 3, 149–161.
3. Sun, Y. et al. (1993) Biotechniques, 15, 372–374.
4. Sarkar, G. et al. (1990) Nucleic Acids Res 18, 7465.