Electrostatic free energy landscapes for nucleic acid helix assembly.
Electrostatic free energy landscapes for nucleic acid helix assembly.
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DOI：
10.1093/nar/gkl810
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发表时间：
2006
影响因子：
14.9
通讯作者：
Chen SJ
中科院分区：
文献类型：
--
作者：
Tan ZJ;Chen SJ
金属离子对核酸折叠至关重要。从自由能景观，我们调查的详细机制，离子诱导的崩溃的范例系统：环栓系短DNA螺旋。我们发现Na+和Mg 2+在螺旋-螺旋组装中起着独特的作用。高[Na+]（>0.3 M）导致螺旋-螺旋静电排斥减少，随后螺旋无序堆积。相比之下，预测浓度> ImM的Mg 2+诱导螺旋-螺旋吸引并导致更紧凑和有序的螺旋-螺旋堆积。Mg 2+在引起核酸压缩方面更有效。此外，自由能景观表明，螺旋之间的束缚环也发挥了重要作用。柔性环，如中性环或高盐浓度下的多核苷酸环，增强螺旋的紧密接近以获得环熵。另一方面，刚性环，例如低盐浓度的多核苷酸环，倾向于使螺旋解压缩。因此，多核苷酸环显著增强了离子诱导的压实转变的锐度。此外，我们发现，在系统中的螺旋数较大或较小的二价离子的半径可以导致更突然的压缩转变和更紧凑的状态在高离子浓度，和离子的尺寸效应变得更加明显，随着螺旋数的增加。
Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na+ and Mg2+ play distinctive roles in helix–helix assembly. High [Na+] (>0.3 M) causes a reduced helix–helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix–helix attraction and results in a more compact and ordered helix–helix packing. Mg2+ is much more efficient in causing nucleic acid compaction. In addition, the free energy landscape shows that the tethering loops between the helices also play a significant role. A flexible loop, such as a neutral loop or a polynucleotide loop in high salt concentration, enhances the close approach of the helices in order to gain the loop entropy. On the other hand, a rigid loop, such as a polynucleotide loop in low salt concentration, tends to de-compact the helices. Therefore, a polynucleotide loop significantly enhances the sharpness of the ion-induced compaction transition. Moreover, we find that a larger number of helices in the system or a smaller radius of the divalent ions can cause a more abrupt compaction transition and a more compact state at high ion concentration, and the ion size effect becomes more pronounced as the number of helices is increased.
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