Mamdouh Wael, Kelly Ross E A, Dong Mingdong, Jacobsen Mikkel F, Ferapontova Elena E, Kantorovich Lev N, Gothelf Kurt V, Besenbacher Flemming
Centre for DNA Nanotechnology, Department of Physics, Aarhus University, Denmark.
J Phys Chem B. 2009 Jun 25;113(25):8675-81. doi: 10.1021/jp9029419.
Self-assembly at the liquid/solid interface of an electrochemically active DNA nucleobase analogue, 1H-benzoimidazole-4,7-dione (Q), has been studied by means of scanning tunneling microscopy (STM). High-resolution STM images revealed the formation of well-ordered two-dimensional (2D) supramolecular nanostructures when the Q molecules are adsorbed onto the graphite surface from a 1-octanol solution. Detailed analysis shows that the observed 2D nanostructures are mainly dominated by hydrogen-bonded Q molecules. Since Q can be considered as a molecule mimicking the nucleobase guanine (G), which is known to form Watson-Crick base pairs with its complementary nucleobase cytosine (C), we have examined the binding ability of Q with C realized by available hydrogen-bonding sites on both Q and C molecules. Upon deposition of a mixture of Q and C molecules onto a graphite surface, one might expect that hydrogen-bonded QC dimers were observed in a new 2D self-assembled structure governed by inter- and intramolecular hydrogen-bonding interactions between Q and C molecules. However, our STM experiments showed that no well-ordered structures are formed and instead phase separation occurs where large-scale homodomains are formed consisting of the individual QQ and CC dimers. To gain further insight into the possible molecular arrangements of the Q and C nucleobases in the mixture phase, the high-resolution STM images are compared with the results from ab initio density functional theory (DFT) calculations.
通过扫描隧道显微镜（STM）研究了电化学活性DNA核碱基类似物1H-苯并咪唑-4,7-二酮（Q）在液/固界面的自组装。高分辨率STM图像显示，当Q分子从1-辛醇溶液吸附到石墨表面时，会形成有序的二维（2D）超分子纳米结构。详细分析表明，观察到的二维纳米结构主要由氢键连接的Q分子主导。由于Q可以被视为模仿核碱基鸟嘌呤（G）的分子，已知G与其互补核碱基胞嘧啶（C）形成沃森-克里克碱基对，因此我们研究了Q与C通过Q和C分子上可用的氢键位点实现的结合能力。将Q和C分子的混合物沉积到石墨表面后，人们可能会预期在由Q和C分子之间的分子间和分子内氢键相互作用控制的新二维自组装结构中观察到氢键连接的QC二聚体。然而，我们的STM实验表明，没有形成有序结构，而是发生了相分离，其中形成了由单个QQ和CC二聚体组成的大规模同型域。为了进一步深入了解混合物相中Q和C核碱基可能的分子排列，将高分辨率STM图像与从头算密度泛函理论（DFT）计算结果进行了比较。
