Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

doi:10.1088/1674-1056/ab5941

中国物理B ›› 2020, Vol. 29 ›› Issue (1): 18701-018701.doi: 10.1088/1674-1056/ab5941

• INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY • 上一篇下一篇

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

Erkun Chen(陈尔坤), Yangtao Fan(范洋涛), Guangju Zhao(赵光菊), Zongliang Mao(毛宗良), Haiping Zhou(周海平), Yanhui Liu(刘艳辉)

1 College of Physics, Guizhou University, Guiyang 550025, China;
2 Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China;
3 Department of Computer Science and Engineering, Shaoxing University, Shaoxing 312000, China

收稿日期:2019-09-06 修回日期:2019-10-26 出版日期:2020-01-05 发布日期:2020-01-05
通讯作者: Haiping Zhou, Yanhui Liu E-mail:hpzhou2885@163.com;ionazati@itp.ac.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11464004 and 11864006), the State Scholarship Fund, China (Grant No. 20173015) and Guizhou Scientific and Technological Program, China (Grant No. 20185781).

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

Erkun Chen(陈尔坤)¹, Yangtao Fan(范洋涛)², Guangju Zhao(赵光菊)¹, Zongliang Mao(毛宗良)¹, Haiping Zhou(周海平)³, Yanhui Liu(刘艳辉)¹

1 College of Physics, Guizhou University, Guiyang 550025, China;
2 Collaborative Innovation Center for Optoelectronic Semiconductors and Efficient Devices, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, China;
3 Department of Computer Science and Engineering, Shaoxing University, Shaoxing 312000, China

Received:2019-09-06 Revised:2019-10-26 Online:2020-01-05 Published:2020-01-05
Contact: Haiping Zhou, Yanhui Liu E-mail:hpzhou2885@163.com;ionazati@itp.ac.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11464004 and 11864006), the State Scholarship Fund, China (Grant No. 20173015) and Guizhou Scientific and Technological Program, China (Grant No. 20185781).

摘要/Abstract

摘要： With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space, Monte Carlo simulations of DNA compaction in free space, in confined spherical space without crowders and in confined spherical space with crowders were performed separately. The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions. In addition, effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii. In confined spherical space without crowders, the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly. In contrast, with the addition of crowders to the confined spherical space, effects of temperature on the phase transition of DNA compaction become insignificant, whereas the phase transition at different temperatures strongly depends on the size of crowder, and the critical volume fraction of crowders pertains to the diameter of crowder linearly.

关键词: macromolecular crowding, Monte Carlo simulation, DNA compaction, phase transition

Abstract: With a view of detecting the effects of macromolecular crowding on the phase transition of DNA compaction confined in spherical space, Monte Carlo simulations of DNA compaction in free space, in confined spherical space without crowders and in confined spherical space with crowders were performed separately. The simulation results indicate that macromolecular crowding effects on DNA compaction are dominant over the roles of multivalent counterions. In addition, effects of temperature on the phase transition of DNA compaction have been identified in confined spherical space with different radii. In confined spherical space without crowders, the temperature corresponding to phase transition depends on the radius of the confined spherical space linearly. In contrast, with the addition of crowders to the confined spherical space, effects of temperature on the phase transition of DNA compaction become insignificant, whereas the phase transition at different temperatures strongly depends on the size of crowder, and the critical volume fraction of crowders pertains to the diameter of crowder linearly.

Key words: macromolecular crowding, Monte Carlo simulation, DNA compaction, phase transition

中图分类号: (Monte Carlo simulations)

87.15.ak

87.16.A- (Theory, modeling, and simulations) 87.15.Cc (Folding: thermodynamics, statistical mechanics, models, and pathways) 87.14.G- (Nucleic acids)

陈尔坤, 范洋涛, 赵光菊, 毛宗良, 周海平, 刘艳辉. Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant[J]. 中国物理B, 2020, 29(1): 18701-018701.

Erkun Chen(陈尔坤), Yangtao Fan(范洋涛), Guangju Zhao(赵光菊), Zongliang Mao(毛宗良), Haiping Zhou(周海平), Yanhui Liu(刘艳辉). Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant[J]. Chin. Phys. B, 2020, 29(1): 18701-018701.

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Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

Phase transition of DNA compaction in confined space: Effects of macromolecular crowding are dominant

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