No abstract

DNA nanotechnology and particularly DNA origami, in which long, single-stranded DNA molecules are folded into predetermined shapes, can be used to form complex self-assembled nanostructures. Although DNA itself has limited chemical, optical or electronic functionality, DNA nanostructures can serve as templates for building materials with new functional properties. Relatively large nanocomponents such as nanoparticles and biomolecules can also be integrated into DNA nanostructures and imaged. Here, we show that chemical reactions with single molecules can be performed and imaged at a local position on a DNA origami scaffold by atomic force microscopy. The high yields and chemoselectivities of successive cleavage and bond-forming reactions observed in these experiments demonstrate the feasibility of post-assembly chemical modification of DNA nanostructures and their potential use as locally addressable solid supports.

The self-assembly of a series of hexadehydrotribenzo[12]annulene (DBA) derivatives has been scrutinized by scanning tunneling microscopy (STM) at the liquid-solid interface. First, the influence of core symmetry on the network structure was investigated by comparing the two-dimensional (2D) ordering of rhombic bisDBA 1a and triangular DBA 2a (Figure 1). BisDBA 1a forms a Kagomé network upon physisorption from 1,2,4-trichlorobenzene (TCB) onto highly oriented pyrolytic graphite (HOPG). Under similar experimental conditions, DBA 2a shows the formation of a honeycomb network. The core symmetry and location of alkyl substituents determine the network structure. The most remarkable feature of the DBA networks is the interdigitation of the nonpolar alkyl chains: they connect the pi-conjugated cores and direct their orientation. As a result, 2D open networks with voids are formed. Second, the effect of alkyl chain length on the structure of DBA patterns was investigated. Upon increasing the length of the alkyl chains (DBAs 3c-e) a transition from honeycomb networks to linear networks was observed in TCB, an observation attributed to stronger molecule-substrate interactions. Third, the effect of solvent on the structure of the nonpolar DBA networks was investigated in four different solvents: TCB as a polar aromatic solvent, 1-phenyloctane as a solvent having both aromatic and aliphatic moieties, n-tetradecane as an aliphatic solvent, and octanoic acid as a polar alkylated solvent. The solvent dramatically changes the structure of the DBA networks. The solvent effects are discussed in terms of factors that influence the mobility of molecules at the liquid-solid interface such as solvation.