Several sequences forming G-quadruplex are highly conserved in regulatory regions of genomes of different organisms and affect various biological processes like gene expression. Diverse G-quadruplex properties can be modulated via their interaction with small polyaromatic molecules such as pyrene. To investigate how pyrene interacts with G-rich DNAs, we incorporated deoxyuridine nucleotide(s) with a covalently attached pyrene moiety (Upy) into a model system that forms parallel G-quadruplex structures. We individually substituted terminal positions and positions in the pentaloop of the c-kit2 sequence originating from the KIT proto-oncogene with Upy and performed a detailed NMR structural study accompanied with molecular dynamic simulations. Our results showed that incorporation into the pentaloop leads to structural polymorphism and in some cases also thermal destabilization. In contrast, terminal positions were found to cause a substantial thermodynamic stabilization while preserving topology of the parent c-kit2 G-quadruplex. Thermodynamic stabilization results from π–π stacking between the polyaromatic core of the pyrene moiety and guanine nucleotides of outer G-quartets. Thanks to the prevalent overall conformation, our structures mimic the G-quadruplex found in human KIT proto-oncogene and could potentially have antiproliferative effects on cancer cells.

中文翻译：

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通过共价探针稳定的 c-kit2 G-四链体：探索 G-四重体不对称

形成 G-四链体的几个序列在不同生物体基因组的调控区域中高度保守，并影响各种生物过程，如基因表达。不同的 G-四链体特性可以通过它们与小多环芳烃分子（如芘）的相互作用来调节。为了研究芘如何与富含 G 的 DNA 相互作用，我们将具有共价连接芘部分 (Upy) 的脱氧尿苷核苷酸掺入形成平行 G-四链体结构的模型系统中。我们分别用 Upy 替换源自 KIT 原癌基因的 c-kit2 序列的五环中的末端位置和位置，并进行了详细的 NMR 结构研究以及分子动力学模拟。我们的结果表明，并入五环会导致结构多态性，在某些情况下还会导致热不稳定。相反，发现末端位置会导致显着的热力学稳定性，同时保留亲本 c-kit2 G-四链体的拓扑结构。热力学稳定性是由芘部分的多环芳核与外部 G-四联体的鸟嘌呤核苷酸之间的 π-π 堆积产生的。由于普遍存在的整体构象，我们的结构模仿了人类 KIT 原癌基因中发现的 G-四链体，并且可能对癌细胞具有抗增殖作用。热力学稳定性是由芘部分的多环芳核与外部 G-四联体的鸟嘌呤核苷酸之间的 π-π 堆积产生的。由于普遍存在的整体构象，我们的结构模仿了人类 KIT 原癌基因中发现的 G-四链体，并且可能对癌细胞具有抗增殖作用。热力学稳定性是由芘部分的多环芳核与外部 G-四联体的鸟嘌呤核苷酸之间的 π-π 堆积产生的。由于普遍存在的整体构象，我们的结构模仿了人类 KIT 原癌基因中发现的 G-四链体，并且可能对癌细胞具有抗增殖作用。