Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine.
Promoter scanning of the human COX-2 gene with 8-ring polyamides: unexpected weakening of polyamide-DNA binding and selectivity by replacing an internal N-Me-pyrrole with β-alanine.
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DOI：
10.1016/j.biochi.2012.09.023
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发表时间：
2013-02
期刊：
影响因子：
3.9
通讯作者：
Wilson, W. David
中科院分区：
文献类型：
--
作者：
Bashkin, James K.;Aston, Karl;Ramos, Joseph P.;Koeller, Kevin J.;Nanjunda, Rupesh;He, Gaofei;Dupureur, Cynthia M.;Wilson, W. David
关键词：
事实证明，聚酰胺DNA识别规则对于在无细胞系统中设计序列选择性DNA结合剂是非常有价值的。然而，这些规则不能完全用于预测细胞、组织或动物的活动，进一步完善我们对DNA识别的理解将有助于生物医学研究。当使用内部β-丙氨酸作为聚酰胺构建块而不是N-甲基吡咯时，也会遇到类似的复杂性；β-丙氨酸被引入到聚酰胺设计中，以保持与目标DNA良好的氢键配准，特别是对于长的聚酰胺或那些具有几个GC BP的聚酰胺(P.B.Dervan，A.R.Urbach，Essay设想。化学。(2001)327-339)。因此，为了阐明分子识别的重要微妙之处，我们研究了在针对Ets-1转录因子设计的8环聚酰胺中用β-丙氨酸取代单一吡咯的效果。用β-丙氨酸取代一个内部的N-甲基吡咯在两个8环聚酰胺中产生β/Im配对导致与dna结合亲和力下降两个数量级并降低dna结合选择性，这与基于文献的预期相反。通过荧光光谱、定量DNA足迹和表面等离子体共振进行了测量，这些截然不同的技术显示出极好的一致性。此外，从小发夹到长dsDNA序列的一系列DNA底物的结果都得到了验证。对接研究帮助表明，与吡咯相比，β-丙氨酸不能与聚酰胺的其余部分或附近的dna进行有效的疏水接触。这些结果有助于改进聚酰胺-DNA识别的设计原则和预期。
Rules for polyamide DNA recognition have proved invaluable for the design of sequence-selective DNA-binding agents in cell-free systems. However, these rules are not fully transferrable to predicting activity in cells, tissues or animals, and additional refinements to our understanding of DNA recognition would help biomedical studies. Similar complexities are encountered when using internal β-alanines as polyamide building blocks in place of N-methyl pyrrole; β-alanines were introduced in polyamide designs to maintain good hydrogen bonding registry with the target DNA, especially for long polyamides or those with several GC bp (P.B. Dervan, A.R. Urbach, Essays Contemp. Chem. (2001) 327–339). Thus, to clarify important subtleties of molecular recognition, we studied the effects of replacing a single pyrrole with β-alanine in 8-ring polyamides designed against the Ets-1 transcription factor. Replacement of a single internal N-methylpyrrole with β-alanine to generate a β/Im pairing in two 8-ring polyamides causes a decrease in DNA binding affinity by two orders of magnitude and decreases DNA binding selectivity, contrary to expectations based on the literature. Measurements were made by fluorescence spectroscopy, quantitative DNA footprinting and surface plasmon resonance, with these vastly different techniques showing excellent agreement. Furthermore, results were validated for a range of DNA substrates from small hairpins to long dsDNA sequences. Docking studies helped show that β-alanine does not make efficient hydrophobic contacts with the rest of the polyamide or nearby DNA, in contrast to pyrrole. These results help refine design principles and expectations for polyamide-DNA recognition.
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影响因子：
2.9
作者：
Dupureur, Cynthia M.;Bashkin, James K.;He, Gaofei
通讯作者：
He, Gaofei
影响因子：
3.5
作者：
Minoshima, Masafumi;Bando, Toshikazu;Sugiyama, Hiroshi
通讯作者：
Sugiyama, Hiroshi
DOI：
10.1073/pnas.0909192106
发表时间：
2009-09-29
影响因子：
11.1
作者：
Muzikar, Katy A.;Nickols, Nicholas G.;Dervan, Peter B.
通讯作者：
Dervan, Peter B.
影响因子：
7.6
作者：
Edwards, Terri G.;Koeller, Kevin J.;Fisher, Chris
通讯作者：
Fisher, Chris
影响因子：
4.8
作者：
Dickinson, LA;Trauger, JW;Gottesfeld, JM
通讯作者：
Gottesfeld, JM