Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
School of Pharmacy, Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun 130117, China.
Molecules. 2020 Jan 17;25(2):387. doi: 10.3390/molecules25020387.
The properties of non-canonical DNA structures, like G-quadruplexes and triplexes, change under cell-mimicking molecular crowding conditions relative to dilute aqueous solutions. The analysis of environmental effects on their stability is crucial since they play important roles in gene expression and regulation. In this study, three intramolecular and intermolecular triplex-forming sequences of different CG-C triplet content (: Hoogsteen base pair; - : Watson-Crick base pair) were designed and their stability measured in the absence and presence of a crowding agent with different K concentrations. In dilute solution, the stability of the triplexes was reduced by decreasing the concentration of KCl. This reduction became smaller as the number of CG-C triplets increased. Under molecular crowding conditions, Watson-Crick base pairs and Hoogsteen base pairs were destabilized and stabilized, respectively. Interestingly, with lower KCl concentrations (≤1 M), the destabilization of the triplexes due to reduction of KCl concentration was significantly smaller than in dilute solutions. In addition, the CG-C content had greater influence on triplex stability under molecular crowding conditions. Our work provides quantitative information about the effects of K concentration on triplex stability under molecular crowding conditions and should further our understanding of the function and regulation of triplexes in bioprocesses.
非 canonical DNA 结构（如 G-四联体和三链体）的性质在模拟细胞的分子拥挤条件下会发生变化，与稀水溶液相比有所不同。分析环境对其稳定性的影响至关重要，因为它们在基因表达和调控中发挥着重要作用。在本研究中，设计了三种不同 CG-C 三联体含量的内分子和外分子三链形成序列（: Hoogsteen 碱基对；-: Watson-Crick 碱基对），并在不存在和存在具有不同 K 浓度的拥挤剂的情况下测量了它们的稳定性。在稀溶液中，三链体的稳定性随着 KCl 浓度的降低而降低。随着 CG-C 三联体数量的增加，这种降低变得更小。在分子拥挤条件下，Watson-Crick 碱基对和 Hoogsteen 碱基对分别被去稳定和稳定。有趣的是，在较低的 KCl 浓度（≤1 M）下，由于 KCl 浓度降低导致的三链体去稳定化作用明显小于稀溶液中的情况。此外，CG-C 含量在分子拥挤条件下对三链体稳定性的影响更大。我们的工作提供了关于 K 浓度对分子拥挤条件下三链体稳定性影响的定量信息，应该进一步加深我们对三链体在生物过程中的功能和调控的理解。
