Department of Biochemistry, Stanford University , Stanford, California 94305, United States.
Department of Chemical Engineering, Stanford University , Stanford, California 94305, United States.
J Am Chem Soc. 2016 Aug 31;138(34):10925-34. doi: 10.1021/jacs.6b04289. Epub 2016 Aug 22.
Electrostatics are central to all aspects of nucleic acid behavior, including their folding, condensation, and binding to other molecules, and the energetics of these processes are profoundly influenced by the ion atmosphere that surrounds nucleic acids. Given the highly complex and dynamic nature of the ion atmosphere, understanding its properties and effects will require synergy between computational modeling and experiment. Prior computational models and experiments suggest that cation occupancy in the ion atmosphere depends on the size of the cation. However, the computational models have not been independently tested, and the experimentally observed effects were small. Here, we evaluate a computational model of ion size effects by experimentally testing a blind prediction made from that model, and we present additional experimental results that extend our understanding of the ion atmosphere. Giambasu et al. developed and implemented a three-dimensional reference interaction site (3D-RISM) model for monovalent cations surrounding DNA and RNA helices, and this model predicts that Na(+) would outcompete Cs(+) by 1.8-2.1-fold; i.e., with Cs(+) in 2-fold excess of Na(+) the ion atmosphere would contain an equal number of each cation (Nucleic Acids Res. 2015, 43, 8405). However, our ion counting experiments indicate that there is no significant preference for Na(+) over Cs(+). There is an ∼25% preferential occupancy of Li(+) over larger cations in the ion atmosphere but, counter to general expectations from existing models, no size dependence for the other alkali metal ions. Further, we followed the folding of the P4-P6 RNA and showed that differences in folding with different alkali metal ions observed at high concentration arise from cation-anion interactions and not cation size effects. Overall, our results provide a critical test of a computational prediction, fundamental information about ion atmosphere properties, and parameters that will aid in the development of next-generation nucleic acid computational models.
静电作用是核酸行为的各个方面的核心，包括它们的折叠、凝聚以及与其他分子的结合，而这些过程的能量学受到围绕核酸的离子氛围的深远影响。鉴于离子氛围的高度复杂和动态性质，理解其性质和影响将需要计算建模和实验之间的协同作用。先前的计算模型和实验表明，离子氛围中的阳离子占有率取决于阳离子的大小。然而，计算模型尚未经过独立测试，并且实验观察到的影响很小。在这里，我们通过实验测试从该模型做出的盲目预测来评估离子大小效应的计算模型，并提供了扩展我们对离子氛围理解的额外实验结果。Giambasu 等人开发并实施了一个用于 DNA 和 RNA 螺旋周围单价阳离子的三维参考相互作用位点（3D-RISM）模型，该模型预测 Na(+) 将以 1.8-2.1 倍的优势取代 Cs(+)；即，在 Cs(+) 是 Na(+) 的 2 倍过量的情况下，离子氛围将包含等量的每种阳离子（核酸研究。2015 年，43,8405）。然而，我们的离子计数实验表明，Na(+) 没有明显优于 Cs(+) 的偏好。在离子氛围中，Li(+) 相对于较大的阳离子具有约 25%的优先占有率，但与现有模型的一般预期相反，其他碱金属离子没有尺寸依赖性。此外，我们跟踪了 P4-P6 RNA 的折叠，并表明在高浓度下观察到的不同碱金属离子的折叠差异源于阳离子-阴离子相互作用，而不是阳离子尺寸效应。总体而言，我们的结果提供了对计算预测的关键测试、关于离子氛围性质的基本信息以及将有助于下一代核酸计算模型发展的参数。
