Tan Zhi-Jie, Chen Shi-Jie
Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
Biophys J. 2006 Feb 15;90(4):1175-90. doi: 10.1529/biophysj.105.070904. Epub 2005 Nov 18.
Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that the TBI theory gives improved predictions for multivalent ions (e.g., Mg2+) than the Poisson-Boltzmann theory. In this study, we use the TBI theory to investigate how the metal ions affect the folding stability of B-DNA helices. We quantitatively evaluate the effects of ion concentration, ion size and valence, and helix length on the helix stability. Moreover, we derive practically useful analytical formulas for the thermodynamic parameters as functions of finite helix length, ion type, and ion concentration. We find that the helix stability is additive for high ion concentration and long helix and nonadditive for low ion concentration and short helix. All these results are tested against and supported by extensive experimental data.
金属离子在核酸的热稳定性和折叠动力学中起着至关重要的作用。对于核酸表面附近的离子（尤其是多价离子），离子间的相关性和离子结合模式的波动可能很重要。泊松 - 玻尔兹曼理论忽略了这些影响，而最近发展的紧密结合离子（TBI）理论则明确考虑了这些影响。大量实验数据表明，与泊松 - 玻尔兹曼理论相比，TBI理论对多价离子（如Mg2 +）能给出更好的预测。在本研究中，我们使用TBI理论来研究金属离子如何影响B - DNA螺旋的折叠稳定性。我们定量评估了离子浓度、离子大小和价态以及螺旋长度对螺旋稳定性的影响。此外，我们推导了作为有限螺旋长度、离子类型和离子浓度函数的热力学参数的实用解析公式。我们发现，对于高离子浓度和长螺旋，螺旋稳定性是可加的；而对于低离子浓度和短螺旋，螺旋稳定性是非加性的。所有这些结果都通过大量实验数据进行了检验并得到了支持。
