Endonuclease V from bacteriophage T4 interacts with its substrate in the minor groove

The interactions between T4 endonuclease and its substrate is observed by using synthetic DNA duplexes having a cis-syn thymine dimer. Oligonucleotides having a methylphosphonate linkage at the thymine dimer site are prepared and their binding with the enzyme is analyzed by the filter-binding method. Changes in the minor groove of DNA duplexes result in the reduction of enzyme binding. The substrate analogue with a methylphosphonate linkage is cleaved for R(sub P) configuration and not for S(sub P) configuration.