A PCR technique, similar to anchored PCR, applied to double-stranded DNA molecules for which the sequence of only one end is known, e.g. in in vivo footprint analysis to detect sites protected by a DNA-binding protein from dimethyl sulphate reaction and thus subject to subsequent chemical cleavage; a specific oligonucleotide is ligated to the unknown end and amplification is accomplished by the PCR procedure using primers complementary to the known end and the newly ligated oligonucleotide.