Part Ⅰ The echinomycin complex with the self-complementary DNA decamer $d(ACGTTAACGT)_2$ has been investigated in solution by proton NMR spectroscopy and compared previously reported complexes, 2echinomycin-$[d(CGTACG)]_2$ and 2echinomycin-$[d(ACGTATACGT)]_2$. Echinomycin binds cooperatively as a bisintercalator at the CpG steps. An analysis of the intermolecular NOE patterns defines the position and orientation of the bound drug molecule. The terminal AㆍT base pairs are Hoogsteen base paired, whereas the four AㆍT pairs are clearly Watson-Crick base paired unlike the other complexes. Thus, the presence of the extra AㆍT base pairs between the binding sites appears to prevent the formation of Hoogsteen base pairs immediately adjacent to the binding site. All four central AㆍT base pairs are destabilized relative to those in the free DNA. Because there is no evidence for unwinding of the DNA duplex in the complex relative to the free DNA, we conclude that the hypersensitivity to DNA cleavage reagents distal to echinomycin binding sites might be due to the destabilization of DNA structure induced by the drug binding.
Part Ⅱ These hyperreactivity of DNA distal to the echinomycin binding sites can not be well explained by the only structural studies. We study one of another properties through measurement imino proton exchange rate. It is the kinetic property of the DNA base pair. We compare the TTAA and TATA steps with base pair lifetimes in complexes and free DNA duplexes. In the duplexes, TTAA step is more stable than TATA step as a whole. But the trends are opposite. The inner most base pairs in TTAA step are less stable than the next base pairs. In the contrary, the inner most base pairs have the slightly longer lifetimes than the next base pairs. Through making complexes with echinomycin, those trend are not changed in each complex , except for slightly destabilization as a whole. We can propose that the propagated destabilization in our result can also explain that hyperreactivity, and one of the important propagated effects may be the enhanced destabilization(increased flexibility) with the structural deviations(unwinding etc.).
Part Ⅲ The local structure of DNA template depends on the sequence. Some specific sequences are recognized by the enzymes to do biological functions. The structures with sequence-specific characters are important to elucidate the interaction of enzyme and DNA. TTAA and TATA are both RNA polymerase binding sites for transcription. For the transcriptional function, the TTAA and TATA steps should be easily unwounded. Because GㆍC base pairs are more stable than AㆍT base pairs, poly AㆍT base pairs may be needed. $(T)_n(A)_n$ and $(TA)_n$ steps may be more easily unwounded than $(A)_n(T)_n$ step due to the stable stacking in $(A)_n(T)_n$. This character may be explained by the structural aspect, stacking, buckling or bending etc., along with the kinetic data. The structural characters of TTAA and TATA steps are well matched to their kinetic data.
