Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove
Stereochemical control of the DNA binding affinity, sequence specificity, and orientation preference of chiral hairpin polyamides in the minor groove
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DOI：
10.1021/ja9737228
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发表时间：
1998-02-25
影响因子：
15
通讯作者：
Dervan, PB
中科院分区：
文献类型：
--
作者：
Herman, DM;Baird, EE;Dervan, PB
含有吡咯 (Py) 和咪唑 (Im) 氨基酸的三环聚酰胺通过 γ-氨基丁酸 (gamma) 共价偶联形成六环发夹，可识别 DNA 小沟中的五碱基对序列。 “γ-转角”的选择性手性取代增强了聚酰胺发夹在 DNA 亲和力和序列特异性方面的特性。制备了核心序列组成ImPyPy-gamma-PyPyPy的聚酰胺，其不同之处在于γ-转角中前手性α-位置的选择性立体化学取代。通过对含有两个匹配位点（5'-TGTTA-3' 和 5'-ACATT-3'）和一个 5'-TGTCA-3' 错配位点的 DNA 片段进行足迹分析和亲和切割，分析了两种对映体聚酰胺的 DNA 结合特性。定量足迹滴定表明，用 (R)-2,4-二氨基丁酸替代 γ-氨基丁酸可将 5'-TGTTA-3' 匹配位点的 DNA 结合亲和力增强 13 倍（K-a = 3.8 x 10(9) M-1）。增强的亲和力是在不影响序列选择性的情况下实现的，事实上，序列选择性相对于单碱基对错配序列 5'-TGTCA-3' 处的结合而言增加了 100 倍。 (S)-2,4-二氨基丁酸连接的发夹结合的亲和力相对于 R 对映异构体降低了 170 倍，而与 5'-ACATT-3' 反向位点相比，序列特异性仅降低了 5 倍。这些效应通过手性胺取代基的乙酰化来调节。这项研究确定了有助于设计具有改进的 DNA 结合亲和力、序列特异性和方向选择性的新型发夹聚酰胺的结构元件。
Three-ring polyamides containing pyrrole (Py) and imidazole (Im) amino acids covalently coupled by gamma-aminobutyric acid (gamma) form six-ring hairpins that recognize five-base-pair sequences in the minor groove of DNA. Selective chiral substitution of the "gamma-turn" enhances the properties of polyamide hairpins with regard to DNA affinity and sequence specificity. Polyamides of core sequence composition ImPyPy-gamma-PyPyPy which differ by selective stereochemical substitution of the prochiral alpha-position in the gamma-turn were prepared. The DNA binding properties of two enantiomeric polyamides were analyzed by footprinting and affinity cleavage on a DNA fragment containing two match sites (5'-TGTTA-3' and 5'-ACATT-3') and one 5'-TGTCA-3' mismatch site. Quantitative footprint titrations demonstrate that replacement of gamma-aminobutyric acid by (R)-2,4-diaminobutyric acid enhances DNA binding affinity for the 5'-TGTTA-3' match site 13-fold (K-a = 3.8 x 10(9) M-1). The enhanced affinity is achieved without a compromise in sequence selectivity, which in fact increases and is found to be 100-fold higher relative to binding at a single base pair mismatch sequence, 5'-TGTCA-3'. An (S)-2,4-diaminobutyric acid linked hairpin binds with 170-fold reduced affinity relative to the R-enantiomer and only 5-fold sequence specificity versus a 5'-ACATT-3' reversed orientation site. These effects are modulated by acetylation of the chiral amine substituents. This study identifies structural elements which should facilitate the design of new hairpin polyamides with improved DNA binding affinity, sequence specificity, and orientational selectivity.