Molecular Dynamics Calculation and X-ray Crystallographic Study of Interaction mode between Plyamine and Z-DNA

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As for the transcription from DNA to t-RNA, it knows that it depends on a state of relaxation of the vector very much. About the transdiption of the vector, it knows that it doesn't happen under the state of super coil. Though a super coil is made to relax, Z-DNA plays a big part. The structure of Z-DNA depends on the kind of the surrounding metal ion concentration, polyamine concentration. We made seven kinds of the complex crystals about polyarnines and d(CG)_3 and succeeded in all the crystallization, and we could get data very expensive resolution up to 1.0Å completely. As a result of x-ray crystallographic analysis of polyamine, N1-{2-[(2-Amino-ethylamino) -ethylamino] -ethyl} -ethane-1,2-diamine and Z-DNA complex crystal, two polyamines went into the minor groove of the Z-DNA completely, and Z-DNA was stabilized.It is the first time to clear the matter that two polyamines combined with the minor groove of Z-DNA at the room temperature by the X-ray crystal structure analysis. We m … More ade the complex crystal of polyamine of thermine N1-[3-(3-Amino-propylamino) -propyl] -propane-1,3-diamine which exists in the living body and d(CG)_3,and as a result of X-ray crystal analysis with a high resolution up to 10 Å, this polyamine connected to the minorgroove of Z-DNA too. It was cleared that two thermine molecules were combined for the minor groove of the d(CG)_3 molecule completely. It is the first time that X-ray crystallographic structural analysis cleared the matter that the natural polyamines combined with Z-DNA at the room temperature. It succeeded in the crystallization of Z-DNA of the long chain d(CG)_6 which nobody succeeded into the crystallization and we did data measurement by SPring-8, and we could collect data up to 1.7 Å resolution. It is the first time that the X-ray crystal structure analysis of the longest Z-DNA could be done. It may introduce the mechanism of relaxation of super coil by Z-DNA. So, we are trying to dear the condition of the B-Z transition by the X-ray crystallographic structure analysis. Therefore using d(CGCGCGAATTCGCGCG) with polyamines which we found stabilize the Z-DNA, we crystallize d(CGCGCGAATTCGCGCG) complexed with these polyamines, and made the combination crystal of Z-DNA and B-DNA. According to these molecules we succeeded in the molecular dynamics calculation. If we can clear the structure by x-ray crystallographic study, we can make the suggestion of B-Z transition mechanism. Less