Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA
Orientation preferences of pyrrole-imidazole polyamides in the minor groove of DNA
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DOI：
10.1021/ja971569b
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发表时间：
1997-09-24
影响因子：
15
通讯作者：
Dervan, PB
中科院分区：
文献类型：
--
作者：
White, S;Baird, EE;Dervan, PB
为了确定吡咯-咪唑（Py-Im）聚酰胺二聚体相对于DNA螺旋中主链的5 '-3'方向是否存在取向偏好，测定了一系列六环发夹聚酰胺的平衡缔合常数（K-a），所述六环发夹聚酰胺在N和C末端的取代方面不同。使用核心序列组成ImPyPy-γ-PyPyPy的发夹聚酰胺与EDTA的亲和切割实验。C-末端的Fe（II）部分显示在每个形式匹配位点5 '-（A，T）G（A，T）（3）-3'和5 '-（A，T）C（A，T）（3）-3'处的单一结合取向。在C-末端的正电荷和在N-末端咪唑的无取代提供了最大的结合取向偏好，由K-a（5 '-TGTTA-3'）/K-a（5 '-TCTTA-3'）计算，每个三环亚基的N-末端朝向靶DNA链的5'侧。去除正电荷、正电荷重排到N-末端或在N-末端咪唑取代降低取向偏好。这些结果表明，第二代设计原则叠加在简单的配对规则，可以进一步优化Py-Im聚酰胺双螺旋DNA的序列特异性。
In order to determine whether there is an orientation preference of pyrrole-imidazole (Py-lm) polyamide dimers with respect to the 5'-3' direction of the backbone in the DNA helix, equilibrium association constants (K-a) were determined for a series of six-ring hairpin polyamides which differ with respect to substitution at the N and C termini. Affinity cleaving experiments using hairpin polyamides of core sequence composition ImPyPy-gamma-PyPyPy with an EDTA . Fe(II) moiety at the C-terminus reveal a single binding orientation at each formal match site, 5'-(A,T)G(A,T)(3)-3' and 5'-(A,T)C(A,T)(3)-3'. A positive charge at the C-terminus and no substitution at the N-terminus imidazole affords the maximum binding orientation preference, calculated from K-a(5'-TGTTA-3')/K-a(5'-TCTTA-3'), with the N-terminal end of each three-ring subunit located toward the 5' side of the target DNA strand. Removal of the positive charge, rearrangement of the positive charge to the N-terminus or substitution at the N-terminal imidazole decreases the orientation preference. These results suggest that second generation design principles superimposed on the simple pairing rules can further optimize the sequence-specificity of Py-Im polyamides for double helical DNA.