Department of Chemical Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States.
J Phys Chem B. 2013 Jan 10;117(1):132-40. doi: 10.1021/jp309523a. Epub 2012 Dec 18.
The single-stranded DNA to single-walled carbon nanotube (SWCNT) hybrid continues to attract significant interest as an exemplary biological molecule-nanomaterial conjugate. In addition to their many biomedical uses, such as in vivo sensing and delivery of molecular cargo, DNA-SWCNT hybrids enable the sorting of SWCNTs according to their chirality. Current experimental methods have fallen short of identifying the actual structural ensemble of DNA adsorbed onto SWCNTs that enables and controls several of these phenomena. Molecular dynamics (MD) simulation has been a useful tool for studying the structure of these hybrid molecules. In recent studies, using replica exchange MD (REMD) simulation we have shown that novel secondary structures emerge and that these structures are DNA-sequence and SWCNT-type dependent. Here, we use REMD to investigate in detail the structural characteristics of two DNA-SWCNT recognition pairs: (TAT)(4)-(6,5)-SWCNT, i.e., DNA sequence TATTATTATTAT bound to the (6,5) chirality SWCNT, and (CCG)(2)CC-(8,7)-SWCNT as well as off-recognition pairs (TAT)(4)-(8,7)-SWCNT and (CCG)(2)CC-(6,5)-SWCNT. From a structural clustering analysis, dominant equilibrium structures are identified and show a right-handed self-stitched motif for (TAT)(4)-(6,5) in contrast to a left-handed β-barrel for (CCG)(2)CC-(8,7). Additionally, characteristics such as DNA end-to-end distance, solvent accessible SWCNT surface area, DNA hydrogen bonding between bases, and DNA dihedral distributions have been probed in detail as a function of the number of DNA strands adsorbed onto the nanotube. We find that the DNA structures adsorbed onto a nanotube are also stabilized by significant numbers of non-Watson-Crick hydrogen bonds (intrastrand and interstrand) in addition to π-π stacking between DNA bases and nanotube surface and Watson-Crick pairs. Finally, we provide a summary of DNA structures observed for various DNA-SWCNT hybrids as a preliminary set of motifs that may be involved in the functional role of these hybrids.
单链 DNA 与单壁碳纳米管（SWCNT）的杂交体继续引起人们的极大兴趣，因为它是一种典型的生物分子-纳米材料缀合物。除了在生物医学领域有许多用途，如活体感应和分子货物的输送外，DNA-SWCNT 杂交体还能够根据其手性对 SWCNT 进行分类。目前的实验方法还未能确定吸附在 SWCNT 上的 DNA 的实际结构组合，而这种结构组合能够实现并控制其中的几种现象。分子动力学（MD）模拟一直是研究这些杂交分子结构的有用工具。在最近的研究中，我们使用复制交换 MD（REMD）模拟表明，新的二级结构出现了，并且这些结构取决于 DNA 序列和 SWCNT 类型。在这里，我们使用 REMD 详细研究了两种 DNA-SWCNT 识别对的结构特征：（TAT）（4）-（6,5）-SWCNT，即与（6,5）手性 SWCNT 结合的 DNA 序列 TATTATTATTAT，以及（CCG）（2）CC-（8,7）-SWCNT 以及非识别对（TAT）（4）-（8,7）-SWCNT 和（CCG）（2）CC-（6,5）-SWCNT。从结构聚类分析中，确定了主要的平衡结构，并显示出（TAT）（4）-（6,5）的右手自缝合基序，而（CCG）（2）CC-（8,7）的左手β-桶。此外，还详细研究了 DNA 端到端距离、溶剂可及的 SWCNT 表面积、DNA 碱基之间的氢键以及 DNA 二面角分布等特性，作为吸附在纳米管上的 DNA 链数的函数。我们发现，吸附在纳米管上的 DNA 结构也通过大量非 Watson-Crick 氢键（链内和链间）以及 DNA 碱基与纳米管表面之间的π-π堆积和 Watson-Crick 对得到稳定。最后，我们提供了各种 DNA-SWCNT 杂合体中观察到的 DNA 结构的摘要，作为这些杂合体功能作用可能涉及的一系列初步基序。
