Generating Nested Deletions with Exonuclease III

  • George Murphy
Part of the Springer Protocols Handbooks book series (SPH)


Exonuclease III (Exo III) will digest double-stranded DNA in a 3′ to 5′ direction if the DNA is blunt ended or possesses a 5′ overhang. It will not digest if there is a 3′ overhang of three or more bases, or if the 3′ end has had thiophosphate-containing bases incorporated into it. In order to generate a set of insert deletions using Exo III, it is necessary to cut the polylinker twice with different restriction enzymes so that the cut end nearest the primer site possesses a 3′ overhang, or has thiophosphate residues at the 3′ end, and the end of the polylinker attached to the insert possesses a 5′ overhang or blunt end. If this can be achieved, digestion with Exo III will result in progressive deletion of the 3′ end of the insert, leaving a single-stranded 5′ overhang that can be removed by treatment with mung bean nuclease (1) or exonuclease VII (Exo VII). The blunt ends thus formed are ligated, a suitable host is transformed, and colonies are picked at random and screened for insert size (2), following which a suitable range of inserts is then sequenced.


Sodium Acetate Luria Bertani Insert Size Digestion Rate Mung Bean Nuclease 
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  1. 1.
    Henikoff, S. (1984) Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene 28, 351–359.PubMedCrossRefGoogle Scholar
  2. 2.
    Wen-Qin, X. and Potts, M. (1989) Quick screening of plasmid deletion clones carrying inserts of desired sizes for DNA sequencing. Gene Anal. Tech. 6, 17–20.CrossRefGoogle Scholar

Copyright information

© Humana Press Inc., Totowa, NJ 2000

Authors and Affiliations

  • George Murphy
    • 1
  1. 1.John Innis Centre for Plant Science ResearchNorwichUK

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