Kodikara Sineth G, Gyawali Prabesh, Gleeson James T, Jákli Antal, Sprunt Samuel, Balci Hamza
Department of Physics, Kent State University, Kent, Ohio 44242, United States.
Advanced Materials and Liquid Crystal Institute, Kent State University, Kent, Ohio 44242, United States.
Biomacromolecules. 2024 Feb 12;25(2):1009-1017. doi: 10.1021/acs.biomac.3c01086. Epub 2024 Jan 2.
The layered liquid crystalline phases formed by DNA molecules, which include rigid and flexible segments ("gapped DNA"), enable the study of both end-to-end stacking and side-to-side (helix-to-helix) lateral interactions, forming a model system to study such interactions at physiologically relevant DNA and ion concentrations. The observed layer structure exhibits long-range interlayer and in-layer positional correlations. In particular, the in-layer order has implications for DNA condensation, as it reflects whether these normally repulsive interactions become attractive under certain ionic conditions. Using synchrotron small-angle X-ray scattering measurements, we investigate the impact of divalent Mg cations (in addition to a constant 150 mM Na) on the stability of the inter- and in-layer DNA ordering as a function of temperature between 5 and 65 °C. DNA constructs with different terminal base pairings were created to mediate the strength of the attractive end-to-end stacking interactions between the blunt ends of the gapped DNA constructs. We demonstrate that the stabilities at a fixed DNA concentration of both interlayer and in-layer order are significantly enhanced even at a few mM Mg concentration. The stabilities are even higher at 30 mM Mg; however, a marked decrease is observed at 100 mM Mg, suggesting a change in the nature of side-by-side interactions within this Mg concentration range. We discuss the implications of these results in terms of counterion-mediated DNA-DNA attraction and DNA condensation.
由DNA分子形成的层状液晶相，其中包括刚性和柔性片段（“间隙DNA”），使得对端对端堆积以及侧向（螺旋对螺旋）横向相互作用的研究成为可能，形成了一个在生理相关的DNA和离子浓度下研究此类相互作用的模型系统。观察到的层结构表现出长程层间和层内位置相关性。特别地，层内有序性对DNA凝聚有影响，因为它反映了这些通常相互排斥的相互作用在某些离子条件下是否会变得具有吸引力。利用同步加速器小角X射线散射测量，我们研究了二价镁阳离子（除了恒定的150 mM钠）在5至65°C温度范围内对层间和层内DNA有序性稳定性的影响。构建了具有不同末端碱基配对的DNA结构，以调节间隙DNA结构钝端之间有吸引力的端对端堆积相互作用的强度。我们证明，即使在几毫摩尔镁浓度下，固定DNA浓度时层间和层内有序性的稳定性也会显著增强。在30 mM镁时稳定性更高；然而，在100 mM镁时观察到明显下降，这表明在该镁浓度范围内侧向相互作用的性质发生了变化。我们根据抗衡离子介导的DNA-DNA吸引力和DNA凝聚来讨论这些结果的意义。
