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Peer-reviewedCC BY 3.0Chemical Science

Multivalent cations stabilize DNA duplexes beyond charge neutralization

  • Yun-Long Chen1
  • Chen-Chen Zheng1,2
  • Yan Zhang3
  • Zhi-Jie Tan1
  • Xing-Hua Zhang1
  1. 1Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, School of Physics and Technology, Women and Children's Hospital, Renmin Hospital of Wuhan University, Wuhan University Wuhan 430072 China
  2. 2School of Physics and Optical Engineering, Zhejiang University of Technology Hangzhou 310023 China
  3. 3Department of Clinical Laboratory, Renmin Hospital of Wuhan University Wuhan China
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Abstract

Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA–protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 kBT/bp for Na+ and increased to 3.98 kBT/bp for protamine, which is a small arginine-rich protein with a highly positive charge (≈21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.

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Cite

BibTeXRIS
BibTeX
@article{chen2026multivalent,
  title = {{Multivalent cations stabilize DNA duplexes beyond charge neutralization}},
  author = {Yun-Long Chen and Chen-Chen Zheng and Yan Zhang and Zhi-Jie Tan and Xing-Hua Zhang},
  journal = {Chemical Science},
  year = {2026},
  month = sep,
  doi = {10.1039/d6sc03808e},
  url = {https://doi.org/10.1039/d6sc03808e},
  note = {CC BY 3.0},
}
RIS
TY  - JOUR
TI  - Multivalent cations stabilize DNA duplexes beyond charge neutralization
AU  - Yun-Long Chen
AU  - Chen-Chen Zheng
AU  - Yan Zhang
AU  - Zhi-Jie Tan
AU  - Xing-Hua Zhang
PY  - 2026
DA  - 2026/09/01
JO  - Chemical Science
DO  - 10.1039/d6sc03808e
UR  - https://doi.org/10.1039/d6sc03808e
AB  - Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA–protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 kBT/bp for Na+ and increased to 3.98 kBT/bp for protamine, which is a small arginine-rich protein with a highly positive charge (≈21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.
SN  - 2041-6520
SN  - 2041-6539
ER  -