Department of Molecular Physics, Faculty of Physics, Yerevan State University , 1 Alex Manoogian Street, Yerevan 375025, Armenia.
Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto , 144 College Street, Toronto, Ontario M5S 3M2, Canada.
J Phys Chem B. 2017 Jul 13;121(27):6511-6519. doi: 10.1021/acs.jpcb.7b03479. Epub 2017 Jun 28.
G-quadruplexes represent a class of noncanonical nucleic acid structures implicated in transcriptional regulation, cellular function, and disease. An understanding of the forces involved in stabilization and destabilization of the G-quadruplex conformation relative to the duplex or single-stranded conformation is a key to elucidating the biological role of G-quadruplex-based genomic switches and the quest for therapeutic means for controlled induction or suppression of a G-quadruplex at selected genomic loci. Solute-solvent interactions provide a ubiquitous and, in many cases, the determining thermodynamic force in maintaining and modulating the stability of nucleic acids. These interactions involve water as well as water-soluble cosolvents that may be present in the solution or in the crowded environment in the cell. We present here the first quantitative investigation of the effect of urea, a destabilizing cosolvent, on the conformational preferences of a G-quadruplex formed by the telomeric d[A(GTA)G] sequence (Tel22). At 20 mM NaCl and room temperature, Tel22 undergoes a two-state urea-induced unfolding transition. An increase in salt mitigates the deleterious effect of urea on Tel22. The urea m-value of Tel22 normalized per change in solvent-accessible surface area, ΔS, is similar to those for other DNA and RNA structures while being several-fold larger than that of proteins. Our results suggest that urea can be employed as an analytical tool in thermodynamic characterizations of G-quadruplexes in a manner similar to the use of urea in protein studies. We emphasize the need for further studies involving a larger selection of G-quadruplexes varying in sequence, topology (parallel, antiparallel, hybrid), and molecularity (monomolecular, bimolecular, tetramolecular) to outline the advantages and the limits of the use of urea in G-quadruplex studies. A deeper understanding of the effect of solvent and cosolvents on the differential stability of the G-quadruplex and duplex conformations is a step toward elucidation of the modulating influence of different types of cosolvents on duplex-G-quadruplex molecular switches triggering genomic events.
G-四链体是一类非经典核酸结构，涉及转录调控、细胞功能和疾病。了解与双链体或单链体构象相比，稳定和破坏 G-四链体构象的力是阐明基于 G-四链体的基因组开关的生物学作用以及寻求控制诱导或抑制所选基因组位点 G-四链体的治疗方法的关键。溶质-溶剂相互作用提供了一种普遍存在的、在许多情况下决定核酸稳定性和调节的热力学力。这些相互作用涉及水以及可能存在于溶液中或细胞拥挤环境中的水溶性共溶剂。我们在这里首次定量研究了脲，一种破坏稳定的共溶剂，对端粒 d[A(GTA)G]序列（Tel22）形成的 G-四链体构象偏好的影响。在 20 mM NaCl 和室温下，Tel22 经历了一个两态脲诱导的展开转变。盐的增加减轻了脲对 Tel22 的有害影响。Tel22 的脲 m 值归一化为溶剂可及表面积的变化，ΔS，与其他 DNA 和 RNA 结构相似，而比蛋白质大几倍。我们的结果表明，脲可以像在蛋白质研究中使用脲一样，作为 G-四链体热力学特性分析的工具。我们强调需要进一步研究涉及更大选择的 G-四链体，这些 G-四链体在序列、拓扑（平行、反平行、杂交）和分子性（单分子、双分子、四分子）方面有所不同，以概述在 G-四链体研究中使用脲的优点和限制。深入了解溶剂和共溶剂对 G-四链体和双链体构象差异稳定性的影响，是阐明不同类型共溶剂对触发基因组事件的双链体-G-四链体分子开关的调节影响的一步。
