Drozdetski Aleksander V, Tolokh Igor S, Pollack Lois, Baker Nathan, Onufriev Alexey V
Department of Physics, Virginia Tech, Blacksburg, Virginia 24061, USA.
Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA.
Phys Rev Lett. 2016 Jul 8;117(2):028101. doi: 10.1103/PhysRevLett.117.028101. Epub 2016 Jul 6.
Increasing the concentration of counterions (salt) is known to reduce the bending persistence length of DNA. Here we use atomistic molecular dynamics simulations to predict that multivalent counterions have the opposite effect on double-stranded RNA, increasing its bending rigidity by at least 30%. This counterintuitive effect is observed for various tri- and tetravalent ions alike, and is robust to methodological details and the RNA sequence. In contrast to DNA, multivalent counterions bind inside the RNA major groove, causing significant contraction of the molecule along its helical axis-as a result, its further deformation due to bending becomes energetically more expensive compared to bending without bound multivalent ions. Thus, the relationship between mechanical properties of a charged polymer and its ionic atmosphere may be richer than previously thought.
众所周知，增加抗衡离子（盐）的浓度会降低DNA的弯曲持久长度。在此，我们使用原子分子动力学模拟预测，多价抗衡离子对双链RNA具有相反的作用，可使其弯曲刚度增加至少30%。对于各种三价和四价离子，均观察到这种违反直觉的效应，并且该效应不受方法细节和RNA序列的影响。与DNA不同，多价抗衡离子结合在RNA的大沟内，导致分子沿其螺旋轴显著收缩，因此，与未结合多价离子时的弯曲相比，其因弯曲而进一步变形在能量上变得更加昂贵。因此，带电聚合物的机械性能与其离子氛之间的关系可能比以前认为的更为丰富。
