中国物理B ›› 2021, Vol. 30 ›› Issue (1): 18702-.doi: 10.1088/1674-1056/abb7f7

所属专题: SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

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  • 收稿日期:2020-06-28 修回日期:2020-08-12 接受日期:2020-09-14 出版日期:2020-12-17 发布日期:2020-12-30

Effect of interaction between loop bases and ions on stability of G-quadruplex DNA

Han-Zhen Qiao(乔汉真), Yuan-Yan Wu(吴园燕)†, Yusong Tu(涂育松)‡, and Cong-Min Ji(祭聪敏)   

  1. College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China
  • Received:2020-06-28 Revised:2020-08-12 Accepted:2020-09-14 Online:2020-12-17 Published:2020-12-30
  • Contact: Corresponding author. E-mail: yywu@yzu.edu.cn Corresponding author. E-mail: ystu@yzu.edu.cn
  • Supported by:
    Project supported by the National Natural Science Foundation of China (Grant Nos. 11705160 and 11647074).

Abstract: G-quadruplexes (GQs) are guanine-rich, non-canonical nucleic acid structures that play fundamental roles in biological processes. The topology of GQs is associated with the sequences and lengths of DNA, the types of linking loops, and the associated metal cations. However, our understanding on the basic physical properties of the formation process and the stability of GQs is rather limited. In this work, we employed ab initio, molecular dynamics (MD), and steered MD (SMD) simulations to study the interaction between loop bases and ions, and the effect on the stability of G-quadruplex DNA, the Drude oscillator model was used in MD and SMD simulations as a computationally efficient manner method for modeling electronic polarization in DNA ion solutions. We observed that the binding energy between DNA bases and ions (K + /Na + ) is about the base stacking free energies indicates that there will be a competition among the binding of M + -base, H-bonds between bases, and the base-stacking while ions were bound in loop of GQs. Our SMD simulations indicated that the side loop inclined to form the base stacking while the loop sequence was Thy or Ade, and the cross-link loop upon the G-tetrads was not easy to form the base stacking. The base stacking side loop complex K + was found to have a good stabilization synergy. Although a stronger interaction was observed to exist between Cyt and K + , such an interaction was unable to promote the stability of the loop with the sequence Cyt.

Key words: G-quadruplex, loop, DNA base, metal ion

中图分类号:  (DNA)

  • 87.14.gk
87.15.-v (Biomolecules: structure and physical properties) 87.15.ag (Quantum calculations) 87.15.ap (Molecular dynamics simulation)