Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

doi:10.1088/1674-1056/22/9/098701

Abstract The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes.

Keywords: DNA condensation multivalent cations molecular dynamics simulation

Received: 22 December 2012
Revised: 15 March 2013
Accepted manuscript online:

PACS:	87.15.-v	(Biomolecules: structure and physical properties)
	36.20.-r	(Macromolecules and polymer molecules)
	82.20.Wt	(Computational modeling; simulation)

Fund: Project supported by the National Natural Science Foundation of China (Grant Nos. 20974081, 20934004, 21174131, and 21104060) and the Zhejiang Provincial Natural Science Foundation of China (Grant No. Y4110357).

Corresponding Authors: Zhang Lin-Xi
E-mail: lxzhang@zju.edu.cn

Cite this article:

Chai Ai-Hua (柴爱华), Ran Shi-Yong (冉诗勇), Zhang Dong (张冬), Jiang Yang-Wei (蒋杨伟), Yang Guang-Can (杨光参), Zhang Lin-Xi (章林溪) Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations 2013 Chin. Phys. B 22 098701

[1]	Jenuwein T and Allis C D 2001 Science 293 1074
[2]	Bednar J, Horowitz R A, Grigoryev S A, Carruthers L M, Hansen J C, Koster A J and Woodcock C L 1998 Proc. Natl. Acad. Sci. USA 95 14173
[3]	Bloomfield V A 1996 Curr. Opin. Struct. Biol. 6 334
[4]	Blessing T, Remy J S and Behr J P 1998 Proc. Natl. Acad. Sci. USA 95 1427
[5]	Montigny W J, Houchens C R, Illenye S, Gilbert J, Coonrod E, Chang Y C and Heintz N H 2001 Nucleic Acids Res. 29 1982
[6]	Ritort F, Mihardja S, Smith S B and Bustamante C 2006 Phys. Rev. Lett. 96 118301
[7]	Zinchenko A A, Yoshikawa K and Baigl D 2005 Phys. Rev. Lett. 95 228101
[8]	Wang Y W, Ran S Y, Man B Y and Yang G C 2011 Soft Matter 7 4425
[9]	Kleideiter G and Nordmeier E 1999 Polymer 40 4013
[10]	Lerman L S 1971 Proc. Natl. Acad. Sci. USA 68 1886
[11]	Vasilevskaya V V, Khokhlov A R, Matsuzawa Y and Yoshikawa K 1995 J. Chem. Phys. 102 6595
[12]	Zhang D, Chai A H, Wen X H, He L L, Zhang L X and Liang H J 2012 Soft Matter 8 2152
[13]	Dai F Y, Wang P F, Wang Y, Tang L, Yang J H, Liu W G, Li H X and Wang G C 2008 Polymer 49 5322
[14]	Li W, Wang P Y, Dou S X and Tong P Q 2003 Chin. Phys. 12 226
[15]	Ran S Y, Wang X L, Fu W B, Lai Z H, Wang W C, Liu X Q, Mai Z H and Li M 2006 Chin. Phys. Lett. 23 504
[16]	Kundu T K and Rao M R S 1995 Biochemistry 34 5143
[17]	Schnurr B, MacKintosh F C and Williams D R M 2000 Europhys. Lett. 51 279
[18]	Ou Z Y and Muthukumar M 2005 J. Chem. Phys. 123 074905
[19]	Bloomfield V A 1997 Biopolymer 44 269
[20]	Fang Y and Hoh J H 1998 Nucleic Acids Res. 26 588
[21]	Cao Q Q, Zuo C C, Ma Y H, Li L J and Zhang Z 2011 Soft Matter 7 506
[22]	Widom J and Baldwin R L 1980 J. Mol. Biol. 144 431
[23]	Widom J and Baldwin R L 1983 Biopolymers 22 1595
[24]	Saminathan M, Thomas T, Shirahata A, Pillai C K S and Thomas T J 2002 Nucleic Acids Res. 30 3722
[25]	Rouzina I and Bloomfield V A 1998 Biophys. J. 74 3152
[26]	Golan R, Pietrasanta L I, Hsieh W and Hansma H G 1999 Biochemistry 38 14069
[27]	Ran S Y, Wang Y W, Yang G C and Zhang L X 2011 J. Phys. Chem. B 115 4568
[28]	Plimpton S 1995 J. Comp. Phys. 117 1
[29]	Deserno M and Holm C 1998 J. Chem. Phys. 109 7678
[30]	Deserno M and Holm C 1998 J. Chem. Phys. 109 7694
[31]	Eastwood J W, Hockney R W and Lawrence D N 1980 Comput. Phys. Commun. 19 215
[32]	Porod G 1949 Monatsh. Chem. 80 251
[33]	Kratky O and Porod G 1949 Recl. Trav. Chim. Pays-Bas. 68 1106
[34]	Li D, Banon S and Biswal S L 2010 Soft Matter 6 4197
[35]	Koslover E F and Spakowitz A J 2009 Phys. Rev. Lett. 102 178102
[36]	Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiöld L 2002 Biophys. J. 82 2860
[37]	Izrailev S, Stepaniants S, Balsera M, Oono Y and Schulten K 1997 Biophys. J. 72 1568
[38]	Kosztin D, Izrailev S and Schulten K 1999 Biophys. J. 76 188
[39]	Shen Y and Zhang L X 2005 J. Polym. Sci. Part B Polym. Phys. 43 223
[40]	Su J Y and Zhang L X 2007 Polymer 48 7419

[1]	Molecular dynamics study of interactions between edge dislocation and irradiation-induced defects in Fe–10Ni–20Cr alloy Tao-Wen Xiong(熊涛文), Xiao-Ping Chen(陈小平), Ye-Ping Lin(林也平), Xin-Fu He(贺新福), Wen Yang(杨文), Wang-Yu Hu(胡望宇), Fei Gao(高飞), and Hui-Qiu Deng(邓辉球). Chin. Phys. B, 2023, 32(2): 020206.
[2]	Adsorption dynamics of double-stranded DNA on a graphene oxide surface with both large unoxidized and oxidized regions Mengjiao Wu(吴梦娇), Huishu Ma(马慧姝), Haiping Fang(方海平), Li Yang(阳丽), and Xiaoling Lei(雷晓玲). Chin. Phys. B, 2023, 32(1): 018701.
[3]	Effect of spatial heterogeneity on level of rejuvenation in Ni₈₀P₂₀ metallic glass Tzu-Chia Chen, Mahyuddin KM Nasution, Abdullah Hasan Jabbar, Sarah Jawad Shoja, Waluyo Adi Siswanto, Sigiet Haryo Pranoto, Dmitry Bokov, Rustem Magizov, Yasser Fakri Mustafa, A. Surendar, Rustem Zalilov, Alexandr Sviderskiy, Alla Vorobeva, Dmitry Vorobyev, and Ahmed Alkhayyat. Chin. Phys. B, 2022, 31(9): 096401.
[4]	Strengthening and softening in gradient nanotwinned FCC metallic multilayers Yuanyuan Tian(田圆圆), Gangjie Luo(罗港杰), Qihong Fang(方棋洪), Jia Li(李甲), and Jing Peng(彭静). Chin. Phys. B, 2022, 31(6): 066204.
[5]	Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations Jian-Gang Wang(王建港), Xiao-Xuan Shi(史晓璇), Yu-Ru Liu(刘玉如), Peng-Ye Wang(王鹏业),Hong Chen(陈洪), and Ping Xie(谢平). Chin. Phys. B, 2022, 31(5): 058702.
[6]	Evolution of defects and deformation mechanisms in different tensile directions of solidified lamellar Ti-Al alloy Yutao Liu(刘玉涛), Tinghong Gao(高廷红), Yue Gao(高越), Lianxin Li(李连欣), Min Tan(谭敏), Quan Xie(谢泉), Qian Chen(陈茜), Zean Tian(田泽安), Yongchao Liang(梁永超), and Bei Wang(王蓓). Chin. Phys. B, 2022, 31(4): 046105.
[7]	Evaluation on performance of MM/PBSA in nucleic acid-protein systems Yuan-Qiang Chen(陈远强), Yan-Jing Sheng(盛艳静), Hong-Ming Ding(丁泓铭), and Yu-Qiang Ma(马余强). Chin. Phys. B, 2022, 31(4): 048701.
[8]	Molecular dynamics simulations of A-DNA in bivalent metal ions salt solution Jingjing Xue(薛晶晶), Xinpeng Li(李新朋), Rongri Tan(谈荣日), and Wenjun Zong(宗文军). Chin. Phys. B, 2022, 31(4): 048702.
[9]	Molecular dynamics simulations on the wet/dry self-latching and electric fields triggered wet/dry transitions between nanosheets: A non-volatile memory nanostructure Jianzhuo Zhu(朱键卓), Xinyu Zhang(张鑫宇), Xingyuan Li(李兴元), and Qiuming Peng(彭秋明). Chin. Phys. B, 2022, 31(2): 024703.
[10]	Comparison of formation and evolution of radiation-induced defects in pure Ni and Ni-Co-Fe medium-entropy alloy Lin Lang(稂林), Huiqiu Deng(邓辉球), Jiayou Tao(陶家友), Tengfei Yang(杨腾飞), Yeping Lin(林也平), and Wangyu Hu(胡望宇). Chin. Phys. B, 2022, 31(12): 126102.
[11]	Learning physical states of bulk crystalline materials from atomic trajectories in molecular dynamics simulation Tian-Shou Liang(梁添寿), Peng-Peng Shi(时朋朋), San-Qing Su(苏三庆), and Zhi Zeng(曾志). Chin. Phys. B, 2022, 31(12): 126402.
[12]	Mechanism of microweld formation and breakage during Cu-Cu wire bonding investigated by molecular dynamics simulation Beikang Gu(顾倍康), Shengnan Shen(申胜男), and Hui Li(李辉). Chin. Phys. B, 2022, 31(1): 016101.
[13]	Non-monotonic temperature evolution of nonlocal structure-dynamics correlation in CuZr glass-forming liquids W J Jiang(江文杰) and M Z Li(李茂枝). Chin. Phys. B, 2021, 30(7): 076102.
[14]	Simulation and experiment of the cooling effect of trapped ion by pulsed laser Chang-Da-Ren Fang(方长达人), Yao Huang(黄垚), Hua Guan(管桦), Yuan Qian(钱源), and Ke-Lin Gao(高克林). Chin. Phys. B, 2021, 30(7): 073701.
[15]	Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex Yun-Qiang Bian(边运强), Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华). Chin. Phys. B, 2021, 30(7): 078702.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Metrics
Related Articles

Processes of DNA condensation induced by multivalent cations：Approximate annealing experiments and molecular dynamics simulations

Cite this article:

Online attention