Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège , B-4000 Liège, Belgium.
J Phys Chem B. 2013 Oct 17;117(41):12391-401. doi: 10.1021/jp406857s. Epub 2013 Sep 10.
Telomeric DNA sequences are particularly polymorphic: the adopted structure is exquisitely sensitive to the sequence and to the chemical environment, for example, solvation. Dehydrating conditions are known to stabilize G-quadruplex structures, but information on how solvation influences the individual rates of folding and unfolding of G-quadruplexes remains scarce. Here, we used electrospray mass spectrometry for the first time to monitor bimolecular G-quadruplex formation from 12-mer telomeric strands, in the presence of common organic cosolvents (methanol, ethanol, isopropanol, and acetonitrile). Based on the ammonium ion distribution, the total dimer signal was decomposed into contributions from the parallel and antiparallel structures to obtain individual reaction rates, and the antiparallel G-quadruplex structure was found to form faster than the parallel one. A dimeric reaction intermediate, in rapid equilibrium with the single strands, was also identified. Organic cosolvents increase the stability of the final structures mainly by increasing the folding rates. Our quantitative analysis of reaction rate dependence on cosolvent percentage shows that organic cosolvent molecules can be captured or released upon G-quadruplex formation, highlighting that they are not inert with DNA. In contrast to the folding rates, the G-quadruplex unfolding rates are almost insensitive to solvation effects, but are instead governed by the sequence and by the final structure: parallel dimers dissociate slower than antiparallel dimers only when thymine bases are present at the 5'-end. These results contribute unraveling the folding pathways of telomeric G-quadruplexes. The solvent effects revealed here enlighten that G-quadruplex structure in dehydrated, and molecularly crowded environments are modulated by the nature of cosolvent (e.g., methanol favors antiparallel structures) due to direct interactions, and by the time scale of the reaction, with >200-fold acceleration of bimolecular G-quadruplex formation in the presence of 60% cosolvent.
端粒 DNA 序列特别具有多态性：所采用的结构对序列和化学环境非常敏感，例如溶剂化。众所周知，脱水条件可以稳定 G-四链体结构，但有关溶剂化如何影响 G-四链体折叠和展开的个别速率的信息仍然很少。在这里，我们首次使用电喷雾质谱法监测 12 个碱基对端粒链的双分子 G-四链体形成，同时存在常见的有机共溶剂（甲醇、乙醇、异丙醇和乙腈）。基于铵离子分布，将总二聚体信号分解为平行和反平行结构的贡献，以获得单个反应速率，并且发现反平行 G-四链体结构比平行结构更快形成。还鉴定了与单链快速平衡的二聚体反应中间体。有机共溶剂主要通过增加折叠速率来增加最终结构的稳定性。我们对反应速率对共溶剂百分比的定量分析表明，在 G-四链体形成时可以捕获或释放有机共溶剂分子，这突出表明它们与 DNA 不是惰性的。与折叠速率相反，G-四链体展开速率几乎不受溶剂化效应的影响，但受序列和最终结构的影响：只有当胸腺嘧啶碱基存在于 5'-端时，平行二聚体的解离速度才比反平行二聚体慢。这些结果有助于阐明端粒 G-四链体的折叠途径。这里揭示的溶剂效应表明，在脱水和分子拥挤的环境中，G-四链体结构受到共溶剂性质（例如，甲醇有利于反平行结构）的调节，这是由于直接相互作用，以及由于反应的时间尺度，在存在 60%共溶剂的情况下，双分子 G-四链体形成的速度提高了 200 多倍。
