Department of Chemical Sciences, University of Naples Federico II , I-80126 Napoli, Italy.
UCL School of Pharmacy, University College London , London WC1N 1AX, United Kingdom.
J Am Chem Soc. 2016 Feb 3;138(4):1226-33. doi: 10.1021/jacs.5b10492. Epub 2016 Jan 19.
We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3' interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3' quadruplex-duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3' end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex-duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3' quadruplex-duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.
我们在此报告了对假定平行排列的 G-四链体与由人类端粒重复序列 TTAGGG 构建的双链 DNA 序列之间形成的 3' 界面复合物的 X 射线晶体学和分子建模研究。我们的晶体学方法提供了端粒 3' 四链体-双链结的详细快照：这个结似乎有可能成为小分子结合和干扰端粒相关功能的独特分子靶标。这个独特的靶标特别相关，因为当前结合假定 G-四链体形成序列的高亲和力化合物很少对特定的四链体具有高度的选择性。在这里，使用不同的假定四链体形成支架在 3' 端连接到端粒双链序列，并退火到互补链，组装了 DNA 结。我们成功地生成了一系列含有 G-四链体-双链体的晶体，无论是单独存在还是存在配体。这些结构证明了平行折叠的 G-四链体和 B 型双链 DNA 的形成。最引人注目的是，结构数据揭示了两个基序之间始终形成 TAT 三联体平台。这个三联体允许碱基的连续堆叠将四链体基序与双链区连接起来。对于这些在没有配体形成的晶体结构中，TAT 三联体界面阻止了配体在 3' 四链体-双链体界面的结合，这与计算机对接预测一致。然而，通过单个核苷酸的重排，可以产生稳定的口袋，从而为界面处选择性分子的结合提供了机会。
