New rapid methods for DNA sequencing based on exonuclease III digestion followed by repair synthesis

Abstract

We describe improve enzymatic methods for sequencing DNA. They are based on partial digestion of duplex DNA with exonuclease III to produce DNA molecules with 3′ ends shortened to varying lengths, followed by repair synthesis to extend and label the 3′ ends. After asymmetrical cleavage of the DNA with a restriction enzyme, the labeled products are separated by gel electrophoresis and the sequence read from the autoradiogram. The entire procedure, beginning with unrestricted DNA and followed through gel electrophoresis, takes only one day for sequencing both strands of the DNA molecule. These methods are especially suitable for sequencing DNA cloned in plasmid vectors, and they greatly extend the usefulness of the dideoxynucleotide chain termination method of Sanger et al. (Proc. Natl. Acad. Sci. USA 74, 5463, 1977). Using these methods we have determined the sequence of a 410 base pair fragment which includes the yeast SUP3 tyrosine tRNA gene.