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Core Concepts
Scientific Fundamentals Explained

Methods for Site-Directed Mutagenesis

Site-directed mutagenesis is an in vitro method for creating a specific mutation in a known sequence, and is typically performed using PCR-based methods. 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. This article describes simple methods for site-directed mutagenesis. For a more detailed overview, see the IDT Mutagenesis Application Guide.

Traditional PCR

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 [1].


Figure 1. Site-Directed Mutagenesis by Traditional PCR. Primers incorporating the desired base changes are used in PCR. As the primers are extended, the mutation is created in the resulting amplicon.

Primer Extension

Site-directed mutagenesis by primer extension involves incorporating mutagenic primers in independent, nested PCRs before combining them in the final product [2]. 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).

Figure 2. Site-Directed Mutagenesis by Primer Extension. (A) Insertion: Primers B and C contain the complementary sequence that will be inserted (blue line). Two reactions are performed in the first round of PCR using primer pairs A/B (1) and C/D (2). The resulting amplicons are mixed with primer pair A/D for the second round of PCR. The complementary ends of the first round amplicons hybridize and the PCR creates the final product with the desired insertion. (B) Deletion: Primers B and C are located on either side of the sequence to be deleted, and contain sequence from both sides of the deletion (black or gray additions that match the black or gray original sequence). Two reactions are performed for the first round of PCR using primer pairs A/B and C/D. The amplicons are mixed with primer pair A/D for the second round of PCR. The overlapping regions of these amplicons hybridize and the PCR creates the final product with the desired deletion.

Inverse PCR

Inverse PCR enables amplification of a region of unknown sequence using primers oriented in the reverse direction [3]. 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.

Figure 3. Site-Directed Mutagenesis by Inverse PCR. The primers used are 5’-phosphorylated to allow ligation of the amplicon ends after PCR. A high fidelity DNA polymerase that creates blunt-ended products is used for the PCR to produce a linearized fragment with the desired mutation, which is then recircularized by intramolecular ligation. (A) Deletion: Primers that hybridize to regions on either side of the area to be deleted are used. (B) Substitution: One of the primers contains the desired mutation (blue bubble). (C) Insertion: The primers hybridize to regions on either side of the location of the desired insertion (black, dotted line). One primer contains the additional sequence that will be inserted (blue line).

IDT Product Focus: Reagents for Mutagenesis


IDT offers custom DNA synthesis on scales from 25 nmole to 10 μmole, and beyond. Every oligonucleotide primer is deprotected and desalted to remove small molecule impurities. Oligonucleotides are quantified twice by UV spectrophotometry to provide an accurate measure of yield and are quality control checked by mass spectrometry.

Same Day Custom Oligos

Ultramer™ Oligonucleotides

Ultramer Oligonucleotides are 25–200 bases long and are synthesized using IDT proprietary, high-fidelity synthesis systems and chemistries. They are the longest, highest-quality oligonucleotides commercially available and are ideal for demanding applications like cloning, ddRNAi, and gene construction. Researchers can save a great deal of time and trouble in these applications through direct synthesis of the entire target fragment. Ultramer Oligonucleotides are available on several scales, and can come with attached modifications such as 5′ phosphate, biotin, and amino modifiers C6 and C12. Internal degenerate bases, as well as deoxyuracil and deoxyInosine modifications are also available.

Learn more about Ultramer Oligos

Phosphate Modifications

Phosphate modifications may be added to any primer or Ultramer Oligonucleotide. 5′ phosphorylation is necessary if the product will be used as a substrate for DNA ligase, as when two pieces will be ligated together to create a combined, longer product. 3′ phosphorylation will inhibit degradation by some 3′-exonucleases and can be used to block extension by many DNA polymerases.


IDT provides a confidential custom gene synthesis service. By ordering genes from IDT, researchers not only save money spent on reagents necessary for construction, cloning, and sequencing, but can also save time by outsourcing the manufacturing of hard-to-clone gene sequences which often results in repeated failures. At IDT, all genes are constructed using Ultramer Oligonucleotides and the highest fidelity next generation synthesis technology available. Genes arrive in a plasmid cloning vector and are ready for use in a variety of applications.

Learn more about Custom Gene Synthesis


  1. Zoller MJ (1991) New molecular biology methods for protein engineering. Curr Opin Biotechnol, 2(4): 526–531.
  2. Reikofski J and Tao BY (1992) Polymerase chain reaction (PCR) techniques for site-directed mutagenesis. Biotechnol Adv, 10(4): 535–547.
  3. Ho SN, Hunt HD, Horton RM, et al. (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene, 77(1):51–59.
  4. Ochman H, Gerber AS, and Hartl DL (1988) Genetic applications of an inverse polymerase chain reaction. Genetics, 120(3): 621–623.

Authors: Jaime Sabel and Nicola Brookman-Amissah are Scientific Writers at IDT.

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