Single-base extension

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Single-base extension (SBE) is a method for determining the identity of a nucleotide base at a specific position along a nucleic acid. The method is used to identify a single-nucleotide polymorphism (SNP).

In the method, an oligonucleotide primer hybridizes to a complementary region along the nucleic acid, to form a duplex, with the primer’s terminal 3’ end directly adjacent to the nucleotide base to be identified. The oligonucleotide primer is enzymatically extended a single base by a nucleotide terminator complementary to the nucleotide being identified. The terminator prevents additional nucleotides from being incorporated. Many approaches can be taken for determining the identity of a terminator, including fluorescence labeling, mass labeling for mass spectrometry, measuring enzyme activity using a protein moiety, and isotope labeling.

The method was invented by Phillip Goelet, Michael Knapp, Richard Douglas and Stephen Anderson while working at the company Molecular Tool. The Illumina Methylation Assay utilizes this method in their Infinium technology to measure DNA methylation levels in the human genome.


  • Philip Goelet, Michael R. Knapp, Stephen Anderson, (1999), U.S. Patent No 5,888,819. Washington, DC: U.S. Patent and Trademark Office.