PCR-based techniques for cloning an unknown DNA fragment adjacent to a known integrant

To understand the mechanism and biological effect of viral or foreign DNA insertions, characterization of DNA sequences which contain the integrant-host junction (IHJ) becomes important. The PCR-based strategy to amplify unknown DNA sequences that flank a known integrant has the advantage of simplicity and alacrity. In general, PCR requires a pair of primers both of which are constructed from a known sequence. This is, however, not applicable to study the integration site of a virus or transposable element since only the DNA sequence of the integrant will be known in advance. To circumvent this problem, a variety of PCR-based techniques have been developed. We attempt in this chapter to summarize these methods and discuss the limitation of each.