Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA

T4 endonuclease V catalyzes the DNA strand cleavage in the vicinity of a thymine dimer. In order to obtain insight into the specific recognition mechanism of this enzyme with a thymine photodimer within DNA, the conformations of five different DNA duplexes, DNA I, d(GCGGATGGCG)-d(CGCCTACCGC), DNA II, d(GCGGTTGGCG)-d(CGCCAACCGC), DNA III, d(GCGGTTGGCG)-d(CGCCAACCGC), DNA IV, d(GCGGGCGGCG)-d(CGCCCGCCGC), and DNA V, d(GCGGCCGGCG)-d(CGCCGGCCGC), with which the enzyme can interact, were studied by 1 H NMR. DNA I, DNA IV, and DNA V do not contain the TT sequence or a thymine dimer and hence, are expected to bind the enzyme only in a nonspecific manner. DNA II includes a single TT sequence which does not form a thymine dimer