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<p>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.</p><p></p>

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Local cation-clamping distorts and softens RNA duplex

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月23日

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  • Chen Zhang,
  • Hai-Long Dong,
  • Jia-Hao Zhang,
  • Liang Dai,
  • Yan Zhang,
  • Zhi-Jie Tan,
  • Xing-Hua Zhang

摘要

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.