Local cation-clamping distorts and softens RNA duplex

Multivalent cations are essential for DNA and RNA structures and their functions. However, how multivalent cations and their accompanying anions jointly reshape nucleic-acid mechanics, and why DNA and RNA respond so differently, remain unclear. Here we show using single-molecule magnetic tweezers that increasing multivalent cation concentrations first softens and then stiffens DNA due to charge inversion, whereas RNA first stiffens and then softens by over twofold. Our all-atom simulations reproduce these effects and reveal a physical mechanism: at low concentrations, multivalent cations clamp the RNA major groove, stiffening RNA; at higher concentrations, anions disrupt this groove clamping and promote local cation-clamping that distorts and softens RNA. The mechanism also explains changes in stretching modulus, contour length, and twist-stretch coupling. Our findings reveal that local cation-clamping sharply softens RNA and highlight the significant roles of anions in modulating RNA structure, providing a framework for tuning nucleic-acid mechanics in vitro for RNA-related applications.