Restriction map of a 35-kb HLA fragment constructed by nested deletion 'drop-out' mapping

Gene. 1995 Oct 27;164(2):335-9. doi: 10.1016/0378-1119(95)00462-f.


An efficient method for generating detailed restriction maps of large cloned DNA segments is demonstrated. The mapping strategy entails comparing restriction fragments from a parent clone and from nested deletion derivatives of that clone. In a set of deletion plasmids of decreasing size, an individual fragment will be lost, or 'drop-out', according to its position in the cloned fragment. In this demonstration, nested deletions were generated in both directions in a 35-kb DNA segment from the human leukocyte antigen (HLA) region by intramolecular transposition of an engineered gamma delta (Tn1000) element present in a special 'deletion factory' cloning vector [Wang et al., Proc. Natl. Acad. Sci. USA 90 (1993) 7874-7878]. Fifteen plasmids with deletions extending in one direction and eleven plasmids with deletions extending in the opposite direction were digested singly by each of four restriction enzymes. A total of 36 cleavage sites were mapped in the 35-kb HLA fragment. This drop-out approach using nested deletions provides a simple and efficient means of mapping restriction sites, genes and other features of interest in cosmid-sized cloned DNA segments or DNAs.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Cloning, Molecular
  • DNA Restriction Enzymes / metabolism
  • DNA Transposable Elements
  • Genetic Techniques
  • HLA Antigens / genetics*
  • Hominidae / genetics*
  • Humans
  • Major Histocompatibility Complex*
  • Mutagenesis
  • Restriction Mapping*
  • Sequence Deletion


  • DNA Transposable Elements
  • HLA Antigens
  • DNA Restriction Enzymes