广西师范大学学报(自然科学版) ›› 2017, Vol. 35 ›› Issue (3): 53-62.doi: 10.16088/j.issn.1001-6600.2017.03.007

• • 上一篇    下一篇

DNA凝聚理论模拟研究

张敏1, 2, 辜凌云1, 2, 周勋1*, 刘艳辉2*   

  1. 1.贵州师范大学物理与电子科学学院,贵州贵阳550025;
    2.贵州大学物理学院,贵州贵阳550025
  • 出版日期:2017-07-25 发布日期:2018-07-25
  • 通讯作者: 周勋(1966—),男,重庆人,贵州师范大学教授,博士。E-mail:hbkfy@gznu.edu.cn
    刘艳辉(1978—),男,吉林四平人,贵州大学教授,博士。E-mail:ionazati@itp.ac.cn
  • 基金资助:
    国家自然科学基金(11047022,11204045,11464004,31360215);贵州大学实验室开放项目(201611);中国博士后面上资助项目(2014M562341);贵州大学青年教师基金(201311);贵州省科学技术基金( 黔科通J合[2006]2004);贵州省优秀科技人才省长基金 (黔省专合字(2009)114)

Simulation Study of DNA Condensation Theory

ZHANG Min1,2,GU Lingyun1,2, ZHOU Xun1*,LIU Yanhui2*   

  1. 1.School of Physics and Electronic Science,Guizhou Normal University,Guiyang Guizhou 550025,China;
    2.College of Physics,Guizhou University,Guiyang Guizhou 550025,China
  • Online:2017-07-25 Published:2018-07-25

摘要: 为进一步揭示DNA凝聚物理机制,基于凝聚反离子强关联性质,本文建立DNA分子凝聚强关联模型并利用Monte Carlo 模拟方法研究DNA分子凝聚的相关性质。凝聚过程中,凝聚构象回转半径出现“台阶式”变化,DNA凝聚过程呈现不连续性;片段自相关定量用来表征DNA凝聚构象中成环数目。凝聚相图表明,DNA凝聚构象大多数为复杂花样结构,凝聚成环的概率较小。凝聚反离子强关联模型较好地揭示了DNA凝聚机制。

关键词: 凝聚反离子, 强关联, DNA凝聚, Monte Carlo 模拟, 回转半径

Abstract: In order to identify the mechanism of DNA condensation further, a strong correlation model is established based on the strong correlation of condensed counterios and Monte Carlo simulation is employed to study the properties of DNA condensation. During the condensation process, gyration radii of condensed conformation appear step-wise manner indicating the discontinuousness of process of DNA condensation. Autocorrelation of the segment reflects the number of loop structure in the condensed conformation, the condensed phase diagram shows the complexity of the condensed conformation, the majority of condensed conformations take on the complex flower structure, and in comparison with flower structure, the occurrence rate of the toroidal structure is small. All the results mentioned above show strong highlight into the mechanism of DNA condensation.

Key words: condensed balanced ions, strong correlation, DNA condensation, Monte Carlo simulation, gyration radius

中图分类号: 

  • Q61
[1] GUO Z, WANG Y, YANG A, et al. The effect of pH on charge inversion and condensation of DNA[J]. Soft Matter, 2016, 12(31): 6669-6674. DOI:10.1039/C6SM01344A.
[2] JIA J L, XI B, RAN S Y. Direct evidence of divalent manganese ion-induced DNA condensation at room temperature[J]. Macromolecular Chemistry and Physics, 2016, 217(14): 1629-1635.DOI:10.1002/macp.201600123.
[3] DEROUCHEY J E, RAU D C. Salt effects on condensed protamine-DNA assemblies:anion binding and weakening of attraction[J].The Journal of Physical Chemistry B, 2011, 115(41):11888.DOI:10.1021/jp203834z.
[4] CARLSTEDTJ, LUNDBERG D, DIAS R S, et al. Condensation and decondensation of DNA by cationic surfactant, spermine, or cationic surfactant-cyclodextrin mixtures: macroscopic phase behavior, aggregate properties, and dissolution mechanisms[J]. Langmuir, 2012, 28(21): 7976-7989.DOI:10.1021/la300266h.
[5] GELBARTW M, BRUINSMA R F, PINCUS P A, et al. DNA-inspired electrostatics[J]. Physics Today, 2000, 53(9): 38-44.DOI:10.1063/1.1325230.
[6] OOSAWA F. Interaction between parallel rodlike macroions[J]. Biopolymers, 1968, 6(11): 1633-1647.DOI: 10.1002/bip.1968.360061108.
[7] MANNING G S. Limiting laws and counterion condensation in polyelectrolyte solutions I. Colligative properties[J]. The Journal of Chemical Physics, 1969, 51(3): 924-933.DOI:10.1063/1.1672157.
[8] LEVIN Y, ARENZON J J, STILCK J F. The nature of attraction between like-charged rods[J]. Physical Review Letters, 1999, 83(13): 2680.DOI:10.1103/PhysRevLett.83.2680.
[9] GRNBECH-JENSEN N, MASHL R J, BRUINSMA R F, et al. Counterion-induced attraction between rigid polyelectrolytes[J]. Physical Review Letters, 1997, 78(12): 2477.DOI:10.1103/PhysRevLett.78.2477.
[10] HA B Y, LIU A J. Counterion-mediated attraction between two like-charged rods[J]. Physical Review Letters, 1997, 79(7): 1289.DOI:10.1103/PhysRevLett.79.1289.
[11] MURAYAMA H, YOSHIKAWA K. Thermodynamics of the collapsing phase transition in a single duplex DNA molecule[J]. The Journal of Physical Chemistry B, 1999, 103(47): 10517-10523.DOI:10.1021/jp990721o.
[12] SAITO T, IWAKI T, YOSHIKAWA K. Why is the compact state of DNA preferred at higher temperature? Folding transition of a single DNA chain in the presence of a multivalent cation[J]. Europhysics Letters, 2005, 71(2): 304.DOI: 10.1209/epl/i2004-10541-6.
[13] KIM W K, NETZ R R. Barrier-induced dielectric counterion relaxation at super-low frequencies in salt-free polyelectrolyte solutions[J]. The European Physical Journal E, 2015, 38(11): 1-15.DOI: 10.1140/epje/i2015-15120-6.
[14] CHREMOS A, DOUGLAS J F. Counter-ion distribution around flexible polyelectrolytes having different molecular architecture[J]. Soft Matter, 2016, 12(11):2932-2941.
[15] DINGM, LIANG Y, LU B S, et al. Charge renormalization and charge oscillation in asymmetric primitive model of electrolytes[J]. Journal of Statistical Physics, 2016, 165(5): 970-989.DOI:10.1007/s10955-016-1644-3.
[16] RITORTF, MIHARDJA S, SMITH S B, et al. Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers[J]. Physical Review Letters, 2006, 96(11):118301.DOI:10.1103/PhysRevLett.96.118301.
[17] COLBY R H, RUBINSTEIN M. Polymer physics[J]. New York: Oxford University, 2003: 274-281.
[18] OOSAWA F. Polyelectrolytes[M]. New York: Marcel Dekker, 1971.
[19] 刘艳辉, 胡林. DNA 微环拓扑性质的 Monte Carlo 模拟[J]. 计算物理, 2009, 26(1): 152-158.
[20] FU W B, WANG X L, ZHANG X H, et al. Compaction dynamics of single DNA molecules under tension[J]. Journal of the American Chemical Society, 2006, 128(47): 15040-15041. DOI:10.1021/ja064305a.
[21] MAO W, LIU Y H, HU L, et al. Effects of ionic dependence of DNA persistence length on the DNA condensation at room temperature[J]. Communications in Theoretical Physics, 2016, 65(5): 639. DOI: 10.1088/0253-6102/65/5/639.
[22] MAO W, GAO Q, LIU Y, et al. Temperature dependence of DNA condensation at high ionic concentration[J]. Modern Physics Letters B, 2016, 30(21):1650298. DOI:10.1142/S0217984916502985.
[23] VILFANI D, CONWELL C C, SARKAR T, et al. Time study of DNA condensate morphology: implications regarding the nucleation, growth, and equilibrium populations of toroids and rods[J]. Biochemistry, 2006, 45(26): 8174-8183. DOI:10.1021/bi060396c.
[24] LAPPALA A, TERENTJEV E M.Maximum compaction density of folded semiflexible polymers[J]. Macromolecules, 2013, 46(17):7125-7131. DOI:10.1021/ma4009127.
[1] 蒋重明, 刘艳辉, 胡林. 早期肿瘤生长模型及其标度律的研究[J]. 广西师范大学学报(自然科学版), 2013, 31(1): 16-20.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!
版权所有 © 广西师范大学学报(自然科学版)编辑部
地址:广西桂林市三里店育才路15号 邮编:541004
电话:0773-5857325 E-mail: gxsdzkb@mailbox.gxnu.edu.cn
本系统由北京玛格泰克科技发展有限公司设计开发