What Is A GC Clamp In PCR Primers?

In this article, I will explain what a GC clamp is in relation to PCR primer design and why they may be useful to include in your primers.

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What is a GC clamp in PCR primer design?

Simply, a GC clamp is the presence of a guanine (G) or cytosine (C) base in the last 5 bases (the 3′ end) of a PCR primer. Having the presence of a GC clamp in a PCR primer can help to improve the specificity of primer binding to the complementary sequence.

The figure below shows an example of a GC clamp in a PCR primer. Note, the GC clamp is highlighted in red (ie the C base).

GC clamp example

Other examples of a GC clamp (in red) in PCR primers include are listed below.


Notice that it does not matter where in the last 5 bases the G or C base is in order for them to be referred to as a GC clamp.

How a GC clamp can improve PCR primer specificity

Binding between G and C bases is formed by three hydrogen bonds, compared to only two between adenine (A) and thymine (T) base pairs. Therefore, G and C base pairs are considered to have stronger binding than A and T base pairs.

Since G and C base pairs have superior binding, placing 1-2 of these bases at the end of the primer will encourage complete primer binding. However, it is not recommended to include >2 G or C bases in the last 5 bases of a primer. Doing so can actually have adverse effects by increasing the primer melting temperature (Tm) and reducing primer specificity.


In sum, a GC clamp is often recommended during PCR primer design in order to encourage complete primer binding to the complementary template. However, too many G or C bases especially at the end of primers can have negative effects.


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