ORDERED DELETIONS FOR DNA SEQUENCING AND INVITRO MUTAGENESIS BY POLYMERASE EXTENSION AND EXONUCLEASE-III GAPPING OF CIRCULAR TEMPLATES

A simple method is described for generating nested deletions from any fixed point in a cloned insert. Starting with a single-stranded phagemid template, T4DNA polymerase is used to extend an annealed primer. This leads to a fully double-stranded circular molecule with a nick or small gap just 5′ to the primer. Exonuclease III initiates progressive digestion from the resulting 3′ end. Removal of timed aliquots and digestion with a single-strand specific endonuclease leads to a series of linear nested fragments having a common end corresponding to the 5′ end of the primer. These molecules are circularized and used to transform cells, providing large numbers of deletion clones with targeted breakpoints. The 6-step procedure involves successive additions to tubes, beginning with a singlestranded template and ending with transformation; no extractions, precipitations or centrifugations are needed. Results are comparable to those obtained with standard Exonuclease Ill-generated deletion protocols, but there is no requirement for restriction endonuclease digestion or for highly purified doublestranded DNA starting material. This procedure provides a strategy for obtaining nested deletions in either direction both for DNA sequencing and for functional analysis. © 1990 Oxford University Press.