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Nucleic Acids Research, 1989, Vol. 17, No. 7 2437-2448
© 1989

MOLECULAR BIOLOGY

Detection of single DNA base differences by competitive oligonucleotide priming

Richard A. Gibbs1,+, Phi-Nga Nguyen2 and C. Thomas Caskey1,2

1Institute for Molecular Genetics, Baylor College of Medicine Houston, TX 77030, USA 2Howard Hughes Medical Institute, Baylor College of Medicine Houston, TX 77030, USA

*To whom correspondence should be addressed

Received January 4, 1989. Accepted February 23, 1989.

Synthetic DNA oligonucleotides can serve as efficient primers for DNA synthesis even when there is a single base mismatch between the primers and the corresponding DNA template. However, when the primer-template annealing is carried out with a mixture of primers and at low stringency the binding of a perfectly matched primer is strongly favored relative to a primer differing by a single base. This primer competition is observed over a range of oligonucleotide sizes from twelve to sixteen bases and with a variety of base mismatches. When coupled with the polymerase chain reaction, for the amplification of specific DNA sequences, competitive oligonucleotide priming provides a simple general strategy for the detection of single DNA base differences.


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