The thermodynamics of polyamide-DNA recognition: Hairpin polyamide binding in the minor groove of duplex DNA
The thermodynamics of polyamide-DNA recognition: Hairpin polyamide binding in the minor groove of duplex DNA
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DOI：
10.1021/bi982628g
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发表时间：
1999-02-16
期刊：
影响因子：
2.9
通讯作者：
Breslauer, KJ
中科院分区：
文献类型：
--
作者：
Pilch, DS;Poklar, N;Breslauer, KJ
含有芳香族氨基酸的新月形合成配体已被设计用于特异性识别DNA小沟中的预定DNA序列。已经开发了将咪唑（Im）和吡咯（Py）氨基酸的并排配对与其预测的靶DNA序列相关联的简单规则。我们在这里报告的六环发夹聚酰胺，ImImPy-gamma-PyPyPy-beta-Dp（其中γ = γ-氨基丁酸，β = β-丙氨酸，和Dp =二甲基氨基丙基酰胺）的DNA结合性能的热力学表征。我们的数据显示，在20 ℃时，该配体以相对适度的1.8倍偏好结合指定的匹配位点5 '-TGTTA-3'，而不是单碱基对错配位点5 '-TGTTA-3'。相反，我们发现配体对它的指定匹配位点的亲和力比双碱基对错配位点5 ′-TATTA-3 ′高102倍。这些结果表明，结合双错配位点的能量成本不一定等于结合单错配位点的能量成本的两倍。我们的量热测量的结合熵和计算的熵数据在20摄氏度揭示了配体序列特异性是同源的。我们已经比较了ImImPy-gamma-PyPyPy-beta-Dp与发夹聚酰胺ImPyPy-gamma-PyPyPy-beta-Dp（Im -> Py“突变体”）的DNA结合性质。我们的数据表明，这两种配体对其指定的匹配位点都表现出高亲和力，这与Dervan配对规则一致。我们的数据还揭示，相对于其相应的单个错配位点，ImImPy-gamma-PyPyPy-beta-Dp对于其指定的匹配位点的选择性低于ImPyPy-gamma-PyPyPy-beta-Dp。这一结果表明，至少在这种情况下，增强的结合亲和力可能伴随着序列特异性的一些损失。这种系统的比较研究，使我们能够开始建立所需的热力学数据库的合理设计的合成聚酰胺与可预测的DNA结合的亲和力和特异性。
Crescent-shaped synthetic ligands containing aromatic amino acids have been designed for specific recognition of predetermined DNA sequences in the minor groove of DNA. Simple rules have been developed that relate the side-by-side pairings of Imidazole (Im) and Pyrrole (Py) amino acids to their predicted target DNA sequences. We report here thermodynamic characterization of the DNA-binding properties of the six-ring hairpin polyamide, ImImPy-gamma-PyPyPy-beta-Dp (where gamma = gamma-aminobutyric acid, beta = beta-alanine, and Dp = dimethylaminopropylamide). Our data reveal that, at 20 degrees C, this ligand binds with a relatively modest 1.8-fold preference for the designated match site, 5'-TGGTA-3', over the single base pair mismatch site, 5'-TGTTA-3'. By contrast, we find that the ligand exhibits a 102-fold greater affinity for its designated match site relative to the double base pair mismatch site, 5'-TATTA-3', These results demonstrate that the energetic cost of binding to a double mismatch site is not necessarily equal to twice the energetic cost of binding to a single mismatch site. Our calorimetrically measured binding enthalpies and calculated entropy data at 20 degrees C reveal the ligand sequence specificity to be enthalpic in origin. We have compared the DNA-binding properties of ImImPy-gamma-PyPyPy-beta-Dp with the hairpin polyamide, ImPyPy-gamma-PyPyPy-beta-Dp (an Im --> Py "mutant"). Our data reveal that both ligands exhibit high affinities for their designated match sites, consistent with the Dervan pairing rules. Our data also reveal that, relative to their corresponding single mismatch sites, ImImPy-gamma-PyPyPy-beta-Dp is less selective than ImPyPy-gamma-PyPyPy-beta-Dp for its designated match site. This result suggests, at least in this case, that enhanced binding affinity can be accompanied by some loss in sequence specificity. Such systematic comparative studies allow us to begin to establish the thermodynamic database required for the rational design of synthetic polyamides with predictable DNA-binding affinities and specificities.