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DNA超分子水凝胶的粗粒化建模与模拟

王曦 黎明 叶方富 周昕

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DNA超分子水凝胶的粗粒化建模与模拟

王曦, 黎明, 叶方富, 周昕

Modelling and simulation of DNA hydrogel with a coarse-grained model

Wang Xi, Li Ming, Ye Fang-Fu, Zhou Xin
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  • DNA超分子水凝胶在生物、医学领域具有广阔的应用前景,基于计算模拟技术研究其分子结构与其宏观性能关系具有重要意义.归因于其复杂的结构和较大的相关时间空间尺度,目前针对DNA水凝胶的分子建模与模拟研究比较缺乏.本文建立了一种DNA水凝胶的粗粒化模型,采用分子动力学模拟的方法针对一种模块化纯DNA水凝胶进行了研究.模拟结果表明其凝胶态介观结构为多孔海绵状,其交联度与水凝胶的浓度成正相关,并得出了其转变温度的范围等.模拟结果与相关实验定性或半定量符合,表明该模型可能用于该模块化DNA水凝胶等类似系统的结构功能关系研究.
    Recently supramolecular hydrogels have become a hot research point in the field of hydrogels. As promising building block for supramolecular hydrogel, DNA has received considerable attention for its designability and excellent mechanical strength, and DNA hydrogel has shown great potential applications in biological and medical areas. To better understand the structure and property of DNA hydrogel, computational simulation is a very powerful tool to complement experimental study. However, owing to the large size of DNA hydrogel system and long time scale of self-assembly process, it is practically unachievable to simulate the system directly at an all-atom level. Coarse-grained simulations should be developed. In this article, we propose a highly coarse-grained model to investigate the mesoscopic structure of well-designed pure DNA hydrogel constructed by Y-shape DNA blocks and linear DNA linkers with sticky ends. In this model, we ignore almost all the atomic details of the building blocks and only give a coarse-grained description of their shapes, and carefully design the Lennard-Jones (LJ) interaction between coarse-grained particles in order to take into account the fact that any of the three arms of a Y block can only interact with a single linker (i.e., the bond is saturated). To design a suitable interaction, here we use a combination of LJ repulsive potential between like particles and LJ attracting potential between unlike particles. Our simulation results show that the hydrogel has two states, namely, homogeneous liquid-like state at high temperature and spongy gel-like state at low temperature. State of this system is related to the degree of cross-linking which is described by average cross-linking pair number per Y-scaffold here. We find that the pair number per Y-scaffold is positively correlated with the concentration of hydrogel blocks, which is consistent with experimental results. We also investigate the distribution of local structure by using voronoi cells, then predict the hole size of the hydrogel network. By the micro-rheology method, we then determine more precisely the value of the transition temperature to be 0.06/kB-0.10/kB, which is also consistent with experimental result. The quantitative relation between transition temperature and binding energy of sticky ends can hopefully provide guidance for the optimal design of DNA hydrogels. The qualitative and even semi-quantitative agreement between our simulation results and experimental results indicates that our coarse-grained model is a suitable and effective one for this pure DNA hydrogel system. The basic ideas of our model can be generalized to more complicated DNA hydrogel systems.
      通信作者: 周昕, xzhou@ucas.ac.cn
    • 基金项目: 国家自然科学基金(批准号:21534007,11675180)资助的课题.
      Corresponding author: Zhou Xin, xzhou@ucas.ac.cn
    • Funds: Project supported by the National Natural Science Foundation of China (Grant Nos.21534007,11675180).
    [1]

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    Yu G, Yan X, Han C, Huang F 2013 Chem. Soc. Rev. 42 6697

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    Topuz F, Okay O 2008 Macromolecules 41 8847

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    Morán M C, Miguel M G, Lindman B 2010 Soft Matter 6 3143

    [5]

    Um S H, Lee J B, Park N, Kwon S Y, Umbach C C, Luo D 2006 Nat. Mater. 5 797

    [6]

    Angioletti-Uberti S, Mognetti B M, Frenkel D 2016 PCCP 18 6373

    [7]

    Li C, Faulkner-Jones A, Dun A R, Jin J, Chen P, Xing Y, Yang Z, Li Z, Shu W, Liu D, Duncan R R 2015 Angew. Chem. Int. Ed. 54 3957

    [8]

    Amiya T, Tanaka T 1987 Macromolecules 20 1162

    [9]

    Topuz F, Okay O 2009 Biomacromolecules 10 2652

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    Starr F W, Sciortino F 2006 J. Phys.: Condens. Mater. 18 L347

    [11]

    Dans P D, Walther J, Gómez H, Orozco M 2016 Curr. Opin. Struct. Biol. 37 29

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    Weiner S J, Kollman P A, Nguyen D T, Case D A 1986 J. Comput. Chem. 7 230

    [13]

    Uusitalo J J, Ingoólfsson H I, Akhshi P, Tieleman D P, Marrink S J 2015 J. Chem. Theory Comput. 11 3932

    [14]

    Collepardo-Guevara R, Schlick T 2014 Proc. Natl. Acad. Sci. USA 111 8061

    [15]

    Xing Y, Cheng E, Yang Y, Chen P, Zhang T, Sun Y, Yang Z, Liu D 2011 Adv. Mater. 23 1117

    [16]

    Cheng E, Xing Y, Chen P, Yang Y, Sun Y, Zhou D, Xu L, Fan Q, Liu D 2009 Angew. Chem. 121 7796

    [17]

    Ouldridge T E, Louis A A, Doye J P K 2010 Phys. Rev. Lett. 104 178101

    [18]

    Lennard-Jones J E 1931 Proc. Phys. Soc. 43 461

    [19]

    SantaLucia J 1998 Proc. Natl. Acad. Sci. USA 95 1460

    [20]

    Schneider T, Stoll E 1978 Phys. Rev. B 17 1302

    [21]

    Okabe A 1992 Spatial Tessellations (New York: John Wiley & Sons) pp362-363

    [22]

    Aurenhammer F 1991 ACM Comput. Surv. 23 345

    [23]

    Winter D, Horbach J 2013 J. Chem. Phys. 138 12A512

    [24]

    Mason T G, Weitz D 1995 Phys. Rev. Lett. 74 1250

    [25]

    Mizuno D, Head D A 2008 Macromolecules 41 7194

    [26]

    Choi S Q, Steltenkamp S, Zasadzinski J A, Squires T M 2011 Nat. Commun. 2 312

    [27]

    Ryckaert J P, Ciccotti G, Berendsen H J C 1977 J. Comput. Phys. 23 327

  • [1]

    Foster J A, Steed J W 2010 Angew. Chem. Int. Ed. 49 6718

    [2]

    Yu G, Yan X, Han C, Huang F 2013 Chem. Soc. Rev. 42 6697

    [3]

    Topuz F, Okay O 2008 Macromolecules 41 8847

    [4]

    Morán M C, Miguel M G, Lindman B 2010 Soft Matter 6 3143

    [5]

    Um S H, Lee J B, Park N, Kwon S Y, Umbach C C, Luo D 2006 Nat. Mater. 5 797

    [6]

    Angioletti-Uberti S, Mognetti B M, Frenkel D 2016 PCCP 18 6373

    [7]

    Li C, Faulkner-Jones A, Dun A R, Jin J, Chen P, Xing Y, Yang Z, Li Z, Shu W, Liu D, Duncan R R 2015 Angew. Chem. Int. Ed. 54 3957

    [8]

    Amiya T, Tanaka T 1987 Macromolecules 20 1162

    [9]

    Topuz F, Okay O 2009 Biomacromolecules 10 2652

    [10]

    Starr F W, Sciortino F 2006 J. Phys.: Condens. Mater. 18 L347

    [11]

    Dans P D, Walther J, Gómez H, Orozco M 2016 Curr. Opin. Struct. Biol. 37 29

    [12]

    Weiner S J, Kollman P A, Nguyen D T, Case D A 1986 J. Comput. Chem. 7 230

    [13]

    Uusitalo J J, Ingoólfsson H I, Akhshi P, Tieleman D P, Marrink S J 2015 J. Chem. Theory Comput. 11 3932

    [14]

    Collepardo-Guevara R, Schlick T 2014 Proc. Natl. Acad. Sci. USA 111 8061

    [15]

    Xing Y, Cheng E, Yang Y, Chen P, Zhang T, Sun Y, Yang Z, Liu D 2011 Adv. Mater. 23 1117

    [16]

    Cheng E, Xing Y, Chen P, Yang Y, Sun Y, Zhou D, Xu L, Fan Q, Liu D 2009 Angew. Chem. 121 7796

    [17]

    Ouldridge T E, Louis A A, Doye J P K 2010 Phys. Rev. Lett. 104 178101

    [18]

    Lennard-Jones J E 1931 Proc. Phys. Soc. 43 461

    [19]

    SantaLucia J 1998 Proc. Natl. Acad. Sci. USA 95 1460

    [20]

    Schneider T, Stoll E 1978 Phys. Rev. B 17 1302

    [21]

    Okabe A 1992 Spatial Tessellations (New York: John Wiley & Sons) pp362-363

    [22]

    Aurenhammer F 1991 ACM Comput. Surv. 23 345

    [23]

    Winter D, Horbach J 2013 J. Chem. Phys. 138 12A512

    [24]

    Mason T G, Weitz D 1995 Phys. Rev. Lett. 74 1250

    [25]

    Mizuno D, Head D A 2008 Macromolecules 41 7194

    [26]

    Choi S Q, Steltenkamp S, Zasadzinski J A, Squires T M 2011 Nat. Commun. 2 312

    [27]

    Ryckaert J P, Ciccotti G, Berendsen H J C 1977 J. Comput. Phys. 23 327

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出版历程
  • 收稿日期:  2017-03-25
  • 修回日期:  2017-04-26
  • 刊出日期:  2017-08-05

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