Tan Zhi-Jie, Chen Shi-Jie
Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
Biophys J. 2007 May 15;92(10):3615-32. doi: 10.1529/biophysj.106.100388. Epub 2007 Feb 26.
A recently developed tightly bound ion model can account for the correlation and fluctuation (i.e., different binding modes) of bound ions. However, the model cannot treat mixed ion solutions, which are physiologically relevant and biologically significant, and the model was based on B-DNA helices and thus cannot directly treat RNA helices. In the present study, we investigate the effects of ion correlation and fluctuation on the thermodynamic stability of finite length RNA helices immersed in a mixed solution of monovalent and divalent ions. Experimental comparisons demonstrate that the model gives improved predictions over the Poisson-Boltzmann theory, which has been found to underestimate the roles of multivalent ions such as Mg2+ in stabilizing DNA and RNA helices. The tightly bound ion model makes quantitative predictions on how the Na+-Mg2+ competition determines helix stability and its helix length-dependence. In addition, the model gives empirical formulas for the thermodynamic parameters as functions of Na+/Mg2+ concentrations and helix length. Such formulas can be quite useful for practical applications.
最近开发的紧密结合离子模型可以解释结合离子的相关性和涨落（即不同的结合模式）。然而，该模型无法处理混合离子溶液，而混合离子溶液在生理上具有相关性且在生物学上具有重要意义，并且该模型基于B-DNA螺旋，因此不能直接处理RNA螺旋。在本研究中，我们研究了离子相关性和涨落在浸入单价和二价离子混合溶液中的有限长度RNA螺旋热力学稳定性上的影响。实验比较表明，与泊松-玻尔兹曼理论相比，该模型给出了改进的预测，泊松-玻尔兹曼理论已被发现低估了诸如Mg2+等多价离子在稳定DNA和RNA螺旋中的作用。紧密结合离子模型对Na+-Mg2+竞争如何决定螺旋稳定性及其螺旋长度依赖性进行了定量预测。此外，该模型给出了作为Na+/Mg2+浓度和螺旋长度函数的热力学参数的经验公式。这些公式在实际应用中可能非常有用。
