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How to Troubleshoot a Primer Dimer

The polymerase chain reaction, or PCR, is a technique in molecular biology used to amplify specific regions of DNA. PCR is dependent on primers, which are short strands of DNA that are complementary and specific to the DNA of interest. While primers generally will bind to DNA matching their sequence, they occasionally will bind to and amplify each other, causing the phenomenon known as a primer dimer.

Things You'll Need

Primer sequences

Instructions

- 1
  Examine the GC content (number of G's and C's) in your primer sequence. GC bonding is stronger than AT bonding because of the additional hydrogen bond between the guanine and cytosine. Optimal bonding is at least 50 percent GC content.
- 2
  Examine the annealing temperature of your reaction. Low annealing temperatures, generally defined as 55 C or below, can cause non-specific binding of the primer, which can cause primer dimers in addition to amplification of incorrect genomic sections.
- 3
  Double-check the amount and concentration of primers you added to the PCR. An excess of primers, generally more than 75 picomoles, can cause primer dimers, as well.

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