Site-directed mutagenesis is an in vitro method for creating a specific mutation in a known sequence. While often performed using PCR-based methods, the availability of custom-designed, synthetic, double-stranded DNA (dsDNA) fragments can drastically reduce the time and steps required to obtain the same sequence changes.
In this article we describe several PCR-based methods for site-directed mutagenesis. Primers designed with mutations can introduce small sequence changes, and primer extension or inverse PCR can be used to achieve longer mutant regions. Using these site-directed mutagenesis techniques allows researchers to investigate the impact of sequence changes or screen a variety of mutants to determine the optimal sequence for addressing the question at hand. The IDT Mutagenesis Application Guide provides more details on these approaches.
Read our follow-up article, Site-directed mutagenesis—improvements to established methods, to learn how to use a simplified, alternative approach for generating similar mutagenesis designs quickly, with custom-designed, dsDNA fragments.
When PCR is used for site-directed mutagenesis, the primers are designed to include the desired change, which could be base substitution, addition, or deletion (Figure 1). During PCR, the mutation is incorporated into the amplicon, replacing the original sequence.
Mutations introduced by PCR can only be incorporated into regions of sequence complementary to the primers and not regions between the primers .
Site-directed mutagenesis by primer extension involves incorporating mutagenic primers in independent, nested PCRs before combining them in the final product . The reaction requires flanking primers (A and D) complementary to the ends of the target sequence, and two internal primers with complementary ends (B and C). These internal primers contain the desired mutation and will hybridize to the region to be altered. During the first round of PCR, the AB and CD fragments are created. These products are mixed for the second round of PCR using primers A and D. The complementary ends of the products hybridize in this second PCR to create the final product, AD, which contains the mutated internal sequence (Figure 2A). Longer insertions can be incorporated by using especially long primers, such as IDT Ultramer™ oligonucleotides.
To create a deletion, the internal primers, B and C, are positioned at either side of the region to be deleted to prevent it from being incorporated within fragments AB and CD from the first round of PCR. The complementary sequences at the ends of the these fragments, created by primers B and C, enable hybridization of AB to CD during the second round of PCR, and the final product with the desired deletion (AD) is created (Figure 2B).
Inverse PCR enables amplification of a region of unknown sequence using primers oriented in the reverse direction . An adaptation of this method can be used to introduce mutations in previously cloned sequences. Using primers incorporating the desired change, an entire circular plasmid is amplified to delete (Figure 3A), change (Figure 3B), or insert (Figure 3C) the desired sequence.