Abstract: Synthetic nucleic acid molecules are provided which are called indexing linkers and which can be selectively linked to unknown, or non-identical cohesive ends of nucleic acid fragments. Such indexing linkers are useful for the selective isolation, identification, amplification, labelling, and modification, of nucleic acid fragments, especially subsets of such fragments released by cleavage using Type IIS restriction endonucleases or restriction endonucleases recognizing interrupted palindromic sequences. Sets of such indexing linker molecules are described which are useful for indexing fragments released by cleavage of a genome. Methods are described for distinguishing such fragments using said indexing linker molecules for effecting detection, or further modification of such fragments; and for amplifying such fragments by the polymerase chain reaction.