2002 Fiscal Year Final Research Report Summary
Molecular Dynamics Calculation and X-ray Crystallographic Study of Interaction mode between Plyamine and Z-DNA
| Project/Area Number |
12672097
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Physical pharmacy
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| Research Institution | Osaka University of Pharmaceutical Sciences |
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Principal Investigator |
OHISHI Hirofumi Osaka University of Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Lecturer, 薬学部, 講師 (00211095)
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| Project Period (FY) |
2000 – 2002
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| Keywords | X-ray crystallographic structure analysis / minor groove / Polyamine / Interaction style / Molecule design / B-Z transition mechanism / Left-handed Z-DNA / long chain left-handed DNA |
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| Research Abstract |
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
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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
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[Publications] Ohishi, Hirofumi, Suzuki, Kenji, Ohtsuchi, Masahiro, Hakoshima, Toshio, Rich, Alexander: "The crystal structure of N1-[2-(2-amino-ethylamino)-ethyl]-ethane-1,2-diamine (polyamines) binding to the minor groove of d(CGCGCG)_2, hexamer at room temperature."FEBS Letters. 523(1-3). 29-34 (2002)
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