Department of Chemistry, Northwestern University, 1145 Sheridan Road, Evanston, Illinois 60208-3113, United States.
ACS Nano. 2012 Sep 25;6(9):8216-25. doi: 10.1021/nn3030139. Epub 2012 Aug 24.
We report a computational search for DNA π-stack structures exhibiting high electric conductance in the hopping regime, based on the INDO/S calculations of electronic coupling and the method of data analysis called k-means clustering. Using homogeneous poly(G)-poly(C) and poly(A)-poly(T) stacks as the simplest structural models, we identify the configurations of neighboring G:C and A:T pairs that allow strong electronic coupling and, therefore, molecular electric conductance much larger than the values reported for the corresponding reference systems in the literature. A computational approach for modeling the impact of thermal fluctuations on the averaged dimer structure was also proposed and applied to the [(G:C),(G:C)] and [(A:T),(A:T)] duplexes. The results of this work may provide guidance for the construction of DNA devices and DNA-based elements of nanoscale molecular circuits. Several factors that cause changes of step parameters favorable to the formation of the predicted stack conformation with high electric conductance of DNA molecules are also discussed; favorable geometries may enhance the conductivity by factors as large as 15.
我们报告了一种基于 INDO/S 电子耦合计算和称为 k-均值聚类的数据分析方法，对表现出跳跃状态下高电导率的 DNA π-堆积结构进行的计算搜索。使用均聚（G）-聚（C）和聚（A）-聚（T）堆积作为最简单的结构模型，我们确定了允许强电子耦合的相邻 G:C 和 A:T 对的构型，从而使分子电导率远远大于文献中报道的相应参考体系的值。还提出了一种用于模拟热波动对平均二聚体结构影响的计算方法，并将其应用于[(G:C),(G:C)]和[(A:T),(A:T)]双链。这项工作的结果可能为构建 DNA 器件和基于 DNA 的纳米级分子电路元件提供指导。还讨论了导致有利于形成具有高电导率的预测堆积构象的阶梯参数变化的几个因素；有利的几何形状可以使电导率提高多达 15 倍。
