logo
AAT Bioquest

What are the guidelines should I follow when designing primers?

Posted August 14, 2023


Answer

Designing the right primer is important in order to achieve successful DNA amplification. For best results, follow these guidelines when designing primers:  

  • Optimal primer length is about 18 to 25 bases. This length is long enough to achieve specific specificity while also allowing primers to bind easily to the template at the annealing temperature. Longer primers may work, but excessively long primers can decrease PCR efficiency.
  • Aim for a GC content of 40-60% in the primer sequence with the 3’ of a primer ending in a G or C to promote binding. This helps maintain stable binding between the primer and the target DNA.
  • The melting temperature (TM) of both forward and reverse primers should be in the range of 55°C - 65°C and within 5°C of each other. This ensures they anneal to the target DNA at a similar temperature, improving PCR efficiency.
  • Avoid having too many G or C bases as this can result in primer-dimer formation. 
  • Choose the annealing temperature (Ta) during PCR based on the Tm of the primers to ensure proper binding and specificity. Annealing temperature that is too high or too low can both affect PCR product yield negatively. 
  • Make sure that the 3' end of the forward primer and the 5' end of the reverse primer do not form complementary sequences, as it may lead to primer-dimer formation.
  • Avoid primers with long runs of a single base as they can misprime. For example, AGCGGGGGATGGGG has runs of base 'G' of value 5 and 4. A maximum acceptable number of runs is 4bp.
  • Avoid intra-primer homology (more than 3 complementary bases within a primer) or inter-primer homology (forward and reverse primers with complementary sequences), as this can lead to self-dimers or primer-dimers instead of binding to the desired DNA sequences. 

Following these guidelines will help you design primers that effectively and specifically amplify the target DNA during PCR. 

Additional resources

Designing PCR Primers for the Amplification-Refractory Mutation System

Polymerase Chain Reaction (PCR)

Helixyte™ Green *20X Aqueous PCR Solution*

Gelite™ Safe DNA Gel Stain *10,000X Water Solution*