Influence of a terminal formamido group on the sequence recognition of DNA by polyamides
Influence of a terminal formamido group on the sequence recognition of DNA by polyamides
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DOI：
10.1021/ja016154b
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发表时间：
2002-03-13
影响因子：
15
通讯作者：
Wilson, WD
中科院分区：
文献类型：
--
作者：
Lacy, ER;Le, NM;Wilson, WD
含有吡咯(Py)-咪唑(Im)的聚酰胺结合在DNA的小凹槽中，可以通过堆积的反平行二聚体识别特定的序列。已经提出有两种不同的低能量方式来形成堆积二聚体，并且这些方式对末端甲酰胺基的存在很敏感：(I)完全重叠堆积模式，其中二聚体的N-末端杂环堆积在C-末端的两个杂环之间的酰胺基团上；以及(Ii)交错堆积模式，其中N-末端杂环在C-末端方向上移动大约一个单位(结构1997，5,1033-1046)。两个不同的DNA序列将被以这两种不同模式堆积的相同聚酰胺识别。尽管聚酰胺作为序列特异性DNA识别剂很重要，但这些堆积的可能性尚未被系统地探索。作为开发能够识别DNA中错配碱基对的试剂的计划的一部分，合成了一组带有和不带有末端甲酰胺基的四个聚酰胺三聚体，并评估了它们在两种不同堆叠模式下与预测的DNA识别序列的相互作用。通过表面等离子体共振(SPIR)检测固定DNA发夹双链的结合，克服了监测DNA与聚酰胺形成络合物的实验困难。SPIR的平衡和动力学结果表明，末端甲酰胺基团对DNA-二聚体络合物的亲和力、序列特异性和形成速率有显著影响。甲酰胺基聚酰胺以交错堆积方式优先结合，而未取代类似物以重叠方式结合。当将末端甲酰胺加到聚酰胺上时，同源DNA序列的亲和力增加约100倍，并且所识别的优选序列也不同。甲酰胺类化合物的缔合和解离速率都较慢，但对解离动力学的影响较大。因此，甲酰胺基团强烈影响聚酰胺与DNA的相互作用，并改变特定聚酰胺堆叠二聚体识别的首选DNA序列。
Pyrrole (Py)-imidazole (Im)-containing polyamides bind in the minor groove of DNA and can recognize specific sequences through a stacked antiparallel dimer. It has been proposed that there are two different low energy ways to form the stacked dimer and that these are sensitive to the presence of a terminal formamido group: (i) a fully overlapped stacking mode in which the N-terminal heterocycles of the dimer stack on the amide groups between the two heterocycles at the C-terminal and (ii) a staggered stacking mode in which the N-terminal heterocycles are shifted by approximately one unit in the C-terminal direction (Structure 1997, 5, 1033-1046). Two different DNA sequences will be recognized by the same polyamide stacked in these two different modes. Despite the importance of polyamides as sequence specific DNA recognition agents, these stacking possibilities have not been systematically explored. As part of a program to develop agents that can recognize mismatched base pairs in DNA, a set of four polyamide trimers with and without terminal formamido groups was synthesized, and their interactions with predicted DNA recognition sequences in the two different stacking modes were evaluated. Experimental difficulties in monitoring DNA complex formation with polyamides were overcome by using surface plasmon resonance (SPIR) detection of the binding to immobilized DNA hairpin duplexes, Both equilibrium and kinetic results from SPIR show that a terminal formamido group has a pronounced effect on the affinity, sequence specificity, and rates of DNA-dimer complex formation. The formamido polyamides bind preferentially in the staggered stacking mode, while the unsubstituted analogues bind in the overlapped mode. Affinities for cognate DNA sequences increase by a factor of around 100 when a terminal formamido is added to a polyamide, and the preferred sequences recognized are also different. Both the association and the dissociation rates are slower for the formamido derivatives, but the effect is larger for the dissociation kinetics. The formamido group thus strongly affects the interaction of polyamides with DNA and changes the preferred DNA sequences that are recognized by a specific polyamide stacked dimer.