Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA.
J Phys Chem B. 2010 Mar 4;114(8):2627-34. doi: 10.1021/jp910395k.
When DNA hybridization is used to link together nanoparticles or molecules, the melting transition of the resulting DNA-linked material often is very sharp. In this paper, we study a particularly simple version of this class of material based on a small-molecule-DNA-hybrid (SMDH) structure that has three DNA strands per 1,3,5-tris(phenylethynyl)benzene core. By varying the concentration of the SMDHs, it is possible to produce either SMDH dimers or bulk aggregates, with the former having highly packed duplex DNA while the latter has an extended network. Melting measurements that we present show that the dimers exhibit sharp melting while the extended aggregates show broad melting. To interpret these results, we have performed coarse-grained molecular dynamics (CGMD) studies of the dimer melting and also of isolated duplex melting using CGMD potentials that have either implicit or explicit ions. Details of the melting simulation technology demonstrate that the simulations properly describe equilibrium transitions in isolated duplexes. The results show that the SMDH dimer has much sharper melting than the isolated duplex. Both implicit and explicit ion calculations show this effect, but the explicit ion results are sharper. An analytical model of the melting thermodynamics is developed which shows that the sharp melting is entropically driven and can be understood primarily in terms of the differences between the effective concentrations of the DNA strands for intracomplex hybridization events compared to intermolecular hybridization.
当 DNA 杂交被用于连接纳米粒子或分子时，所得 DNA 连接材料的熔融转变通常非常陡峭。在本文中，我们研究了基于具有每 1,3,5-三(苯乙炔基)苯核的三个 DNA 链的小分子-DNA 杂交 (SMDH) 结构的此类材料的一个特别简单的版本。通过改变 SMDH 的浓度，可以产生 SMDH 二聚体或块状聚集体，前者具有高度堆积的双链 DNA，而后者具有扩展的网络。我们呈现的熔融测量表明，二聚体表现出尖锐的熔融，而扩展的聚集体表现出宽的熔融。为了解释这些结果，我们对二聚体的熔融以及使用具有隐式或显式离子的 CGMD 势的孤立双链的熔融进行了粗粒度分子动力学 (CGMD) 研究。熔融模拟技术的细节表明，模拟正确描述了孤立双链的平衡转变。结果表明，SMDH 二聚体的熔融比孤立双链更陡峭。隐式和显式离子计算都显示出这种效果，但显式离子的结果更陡峭。开发了一个熔融热力学的分析模型，表明尖锐的熔融是由熵驱动的，并且可以主要根据与分子间杂交相比，内复合物杂交事件中 DNA 链的有效浓度的差异来理解。
