Studies of surface coverage and orientation of DNA molecules immobilized onto preformed alkanethiol self-assembled monolayers

DNA molecules are attached onto carboxylate-terminated alkanethiol self-assembled monolayers (SAMs) preformed at gold surfaces via the N-hydroxysulfosuccinimide (NHS)/1-(3-(dimethylamino)propyl)-3-ethylcarbodiimide hydrochloride (EDC) cross-linking reaction. Cyclic voltammetry, quartz crystal microbalance (QCM), and atomic force microscopy (AFM) were used to probe the surface coverage and molecular orientation of the immobilized DNA molecules. The DNA attachment is attributed to the formation of amide bond between the carboxylate groups and the amino groups on the DNA bases since the possibility of nonspecific adsorption of DNA onto preformed SAMs or NHS ester monolayers was studied and excluded. Our voltammetric results indicate a significant blockage of the sites originally available in the alkanethiol SAMs for facile heterogeneous electron transfer by the attached DNA molecules. QCM provided a semiquantitative measurement of the amount of immobilized DNA. The AFM images, for the first time, revealed that relatively ordered DNA films can be formed in the covalent attachment with DNA molecules stretched by the underlying terminal carboxylate groups of the SAMs. However, certain fragmentation appears to have occurred upon immobilization. The fragmentation is probably due to the strong interaction between the DNA molecules and the carboxylate groups whose spatial distribution does not fit perfectly well with the separation and distribution of the amino groups on the bases within the DNA double helix.