Garabet Arees, Prislan Iztok, Poklar Ulrih Nataša, Wells James W, Chalikian Tigran V
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, ON M5S 3M2, Canada.
Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia.
Biomolecules. 2025 Mar 26;15(4):483. doi: 10.3390/biom15040483.
G-quadruplexes and -motifs are four-stranded non-canonical structures of DNA. They exist in the cell, where they are implicated in the conformational regulation of cellular events, such as transcription, translation, DNA replication, telomere homeostasis, and genomic instability. Formation of the G-quadruplex and -motif conformations in the genome is controlled by their competition with the pre-existing duplex. The fate of that competition depends upon the relative stabilities of the competing conformations, leading ultimately to a distribution of double helical, tetrahelical, and coiled conformations that coexist in dynamic equilibrium with each other. We previously developed a CD spectroscopy-based procedure to characterize the distribution of conformations adopted by equimolar mixtures of complementary G- and C-rich DNA strands from the promoter regions of the c-MYC, VEGF, and Bcl-2 oncogenes. In those bimolecular systems, duplex-to-tetraplex and duplex-to-coil transitions are accompanied by strand separation and an associated entropic cost. This situation is distinct from the pseudo-monomolecular nature of conformational transformations within the genome, where strand separation does not occur. To mimic better the situation in the genome, we here extend our studies to a monomolecular DNA construct-a hairpin-in which complementary G- and C-rich strands featuring sequences from the promoter region of the c-MYC oncogene are linked by a dT loop. We used our CD-based procedure to quantify the distribution of conformational states sampled by the hairpin at pH 5.0 and 7.0 as a function of temperature and the concentration of KCl. The data were analyzed according to a thermodynamic model based on equilibria between the different conformational states to evaluate the thermodynamic properties of the duplex-to-coil, G-quadruplex-to-coil, and -motif-to-coil transitions of the hairpin. The results have implications for the modulation of such transitions as a means of therapeutic intervention.
G-四链体和G-基序是DNA的四链非经典结构。它们存在于细胞中，参与细胞活动的构象调控，如转录、翻译、DNA复制、端粒稳态和基因组不稳定性。基因组中G-四链体和G-基序构象的形成受其与预先存在的双链体竞争的控制。这种竞争的结果取决于竞争构象的相对稳定性，最终导致双螺旋、四螺旋和卷曲构象以动态平衡的方式共存。我们之前开发了一种基于圆二色光谱的方法，用于表征来自c-MYC、VEGF和Bcl-2癌基因启动子区域的富含G和C的互补DNA链等摩尔混合物所采用的构象分布。在这些双分子系统中，双链体到四链体和双链体到卷曲的转变伴随着链的分离以及相关的熵成本。这种情况与基因组内构象转变的假单分子性质不同，在基因组内不会发生链的分离。为了更好地模拟基因组中的情况，我们在此将研究扩展到一种单分子DNA构建体——发夹结构，其中来自c-MYC癌基因启动子区域的富含G和C的互补链通过一个dT环连接。我们使用基于圆二色光谱的方法来量化发夹结构在pH 5.0和7.0下作为温度和KCl浓度函数所采样的构象状态分布。根据基于不同构象状态之间平衡的热力学模型对数据进行分析，以评估发夹结构从双链体到卷曲、从G-四链体到卷曲以及从G-基序到卷曲转变的热力学性质。这些结果对于调节此类转变作为一种治疗干预手段具有重要意义。
