The attachment of DNA strands to gold surfaces is performed in many devices, such as various DNA sensors. One of the standard methods used to immobilize DNA on gold surfaces involves two steps: the attachment of a thiol linker group (usually in the form of alkanethiol moiety) to the DNA strand, and the chemical reaction between the thiol-terminated DNA and the gold surface. Since thiols react chemically with the surface of gold substrates, forming very stable Au-S bonds, it is often assumed that the chemisorption on the gold surface of nucleotides with an attached thiol linker group leads to the formation of an order layer with the linking moieties relatively densely packed on the gold surface. In this contribution we show that chemisorption of thiolated mononucleotides does not occur according to this model. For example, the thiolated mononucleotide containing adenine strongly interacts with the gold surface via the adenine moiety. Moreover, bonding of the mononucleotide containing adenine to the gold surface is relatively similar to the bonding of adenine, and the main difference is that the adenine interacts with the gold surface mainly through the pyrimidine ring, while for adenine mononucleotide interaction via the imidazole ring also significantly contributes to the total bonding. A similar effect was observed for the mononucleotide containing cytosine, and the main difference between the interaction with the gold surface of cytosine and cytosine mononucleotide is that mononucleotide containing cytosine interacts with the gold surface to a significantly larger extend via the carboxylic group of the base. We also show that the structure of the layer formed on the gold surface by the thiolated mononucleotides may be significantly different than the structure of the layer formed by thiolated single-stranded DNA containing even as few as two bases.
Keywords: DNA; Raman spectroscopy; SERS; alkanethiols; mononucleotides; surface-enhanced Raman spectroscopy.