Effects of the N-terminal acylamido group of imidazole- and pyrrole-containing polyamides on DNA sequence specificity and binding affinity.
Effects of the N-terminal acylamido group of imidazole- and pyrrole-containing polyamides on DNA sequence specificity and binding affinity.
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含咪唑和吡咯的聚酰胺的 N 端酰胺基对 DNA 序列特异性和结合亲和力的影响。
DOI：
10.1021/bi900242t
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发表时间：
2009
期刊：
影响因子：
2.9
通讯作者：
J. Hartley
中科院分区：
文献类型：
--
作者：
L. Westrate;Hilary Mackay;T. Brown;Binh Nguyen;J. Kluza;W. Wilson;Moses Lee;J. Hartley
含咪唑和吡咯的聚酰胺上的N-末端甲酰胺基导致堆叠的聚酰胺以交错基序结合在DNA的小沟中，并且与非甲酰胺基化合物相比，它还增加了结合亲和力。为了进一步研究N-末端酰氨基在影响序列特异性和结合亲和力中的作用，设计并合成了六种含有核心三杂环结构IPI的聚酰胺类似物，本文报道的酰氨基部分包括以下：甲酰氨基（f-IPI，1），乙酰氨基（Ac-IPI，2），三氟乙酰氨基（Tf-IPI，3）、N-甲基脲基（Mu-IPI，4）、N-甲基吡咯-2-甲酰胺基（PIPI，5）和（13）C-标记的甲酰胺基-IPI化合物（（13）C-f-IPI，6）。此外，还合成了两种非酰化的IPI化合物，即含氨基（NH（2）-IPI，7）和非甲酰氨基（nf-IPI，8）化合物。利用分子生物学和生物化学方法研究了化合物1-8的结合特性，包括生物物理技术，如DNA熔融、圆二色性、等温滴定量热、表面等离子体共振和DNase I足迹。除nf-IPI和NH（2）-IPI外，所有其他化合物均优先与同源序列5 '-ACGCGT-3'相互作用。生物物理结果表明，所有六种化合物结合在小沟内，在其同源DNA序列的堆叠，交错，反平行二聚体。从最高到最低结合亲和力的顺序如下：f-IPI > P-IPI > Ac-IPI > Mu-IPI > Tf-IPI >> NH（2）和nf-IPI。因此，在N-末端具有酰氨基部分对于聚酰胺以堆叠和交错的基序与DNA结合是重要的。根据足迹分析，与f-IPI（1）相比，P-IPI（5）、Ac-IPI（2）、Mu-IPI（4）和Tf-IPI（3）对其同源物5 '-ACGCGT-3'的序列偏好性表现出一些增强。[（13）C]f-IPI-CGCGnmr复合物的NMR分析显示甲酰胺基（13）C信号的轻微低场位移，表明该部分保持完整。结合亲和力的趋势表明，空间因素发挥了作用，其中小的和平面的芳族酰氨基单元，如f，Ac和P是优选的。与Ac-IPI（2）相比，诸如Mu-IPI（4）和Tf-IPI（3）中的极性基团对结合亲和力产生负面影响。
The N-terminal formamido group on imidazole- and pyrrole-containing polyamides causes stacked polyamides to bind in the minor groove of DNA in the staggered motif, and it also increases the binding affinity compared to those of non-formamido compounds. To further investigate the role of the N-terminal acylamido in affecting sequence specificity and binding affinity, six polyamide analogues containing the core triheterocyclic structure IPI were designed and synthesized, and the acylamido moiety reported herein includes the following: formamido (f-IPI, 1), acetamido (Ac-IPI, 2), trifluoroacetamido (Tf-IPI, 3), N-methylureido (Mu-IPI, 4), N-methylpyrrole-2-carboxamido (PIPI, 5), and the (13)C-labeled formamido-IPI compound ((13)C-f-IPI, 6). In addition, two nonacylated IPI compounds were also synthesized and examined, namely, the amino-containing (NH(2)-IPI, 7) and non-formamido (nf-IPI, 8) compounds. The binding characteristics of compounds 1-8 were investigated using methods of molecular biology and biochemistry, which included biophysical techniques, such as DNA melts, circular dichroism, isothermal titration calorimety, and surface plasmon resonance and DNase I footprinting. With the exception of nf-IPI and NH(2)-IPI, all other compounds preferentially interacted with the cognate sequence, 5'-ACGCGT-3'. The biophysical results suggest that all six compounds bind within the minor groove at their cognate DNA sequence as stacked, staggered, antiparallel dimers. The order from highest to lowest binding affinities is as follows: f-IPI > P-IPI > Ac-IPI > Mu-IPI > Tf-IPI >> NH(2) and nf-IPI. Hence, having an acylamido moiety at the N-terminus is important for the binding of polyamides to DNA in a stacked and staggered motif. According to footprinting analysis, P-IPI (5), Ac-IPI (2), Mu-IPI (4), and Tf-IPI (3) exhibited some enhancement in sequence preference for their cognate 5'-ACGCGT-3' over f-IPI (1). NMR analysis of the [(13)C]f-IPI-CGCGnmr complex showed a slight downfield shift in the formamido (13)C signal indicating that the moiety remained intact. The trend in binding affinity suggests that steric factors play a role, in which small and planar aromatic acylamido units such as f, Ac, and P are preferred. Polar groups, such as in Mu-IPI (4) and Tf-IPI (3), afforded negative effects on binding affinity, compared to that of Ac-IPI (2).
咪唑-咪唑对作为 T:G 错配碱基对的小沟识别基序。
影响因子：
14.9
作者：
Yang,XL;Hubbard,RB;Lee,M;Tao,ZF;Sugiyama,H;Wang,AH
通讯作者：
Wang,AH
影响因子：
3.5
作者：
Mackay, Hilary;Brown, Toni;Uthe, Peter B.;Westrate, Laura;Sielaff, Alan;Jones, Justin;Lajiness, James P.;Kluza, Jerome;O'Hare, Caroline;Nguyen, Binh;Davis, Zach;Bruce, Chrystal;Wilson, W. David;Hartley, John A.;Lee, Moses
通讯作者：
Lee, Moses
影响因子：
15
作者：
Lacy, ER;Le, NM;Wilson, WD
通讯作者：
Wilson, WD