The cloning vector pMCS5 contains the ultimate multiple cloning site (MCS) with 59 unique restriction sites. The recognition sites for many commonly used restriction enzymes are included, providing a suitable cloning site for almost any application. This vector contains 46 unique hexamer sites, 2 heptamer sites and the recognition sites for all ten known octanucleotide-specific endonucleases. The well-defined 18-mer sequence of the extremely rarely cutting enzyme I-SceI is located at one terminus of the MCS, enabling the linearization of recombinant clones. I-SceI does not recognize a palindrome and can thus be used for labeling and end-cloning. It can also be used for strand protection in unidirectional deletion experiments. Additionally, the MCS also restriction sites that occur very infrequently in human DNA such as MluI, NruI and SplI.