The invention provides criteria and methods for selecting optimum
subsequence(s) from a target gene for targeting by a zinc finger protein.
Some of the methods of target site selection seek to identify one or more
target segments having a DNA motif containing one or more so-called
D-able subsites having the sequence 5'NNGK3'. Other methods of the
invention are directed to selection of target segments within target
genes using a correspondence regime between different triplets of three
bases and the three possible positions of a triplet within a nine-base
site. In another aspect, the invention provides methods of designing zinc
finger proteins that bind to a preselected target site. These methods can
be used following the preselection of target sites according to the
procedures and criteria described above. The methods of design use a
database containing information about previously characterized zinc
finger proteins.