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We investigate interactions between counterions and single-stranded DNA (ssDNA) immobilized on gold. X-ray photoelectron spectroscopy (XPS) is the main technique that we use to quantify the amount of counterions (Na+, K+, Ca2+) and the effects they have on the formation and structure of ssDNA monolayers. Additional chemical and structural information is provided by the Fourier transform infrared (FTIR) and near-edge x-ray absorption fine structure (NEXAFS) spectroscopies. We rely on surface plasmon resonance (SPR) imaging spectroscopy and quartz crystal microbalance (QCM) measurements to provide in situ information. We find two model systems to be particularly useful for studying interactions between counterions and DNA. First, monolayers of thiol-modified thymine homo-oligonucleotides on gold are convenient model systems, because they allow quantitative analysis of the surface density and conformation based on spectroscopic data. A second, unique, class of ssDNA monolayers is formed by ssDNA having sequences that follow the d(Ak-Tm-Nn) pattern. The surface density and brush-like conformation of monolayers formed by these block-oligonucleotides can be deterministically and independently controlled. Our experimental results show that interactions between counterions and ssDNA are both significant and important. Specifically, we find that both the concentration and identity of the counterion present in solution strongly influence the process of ssDNA immobilization, the structure, and the stability of the resulting ssDNA monolayers. The most dramatic differences are observed between divalent and monovalent counterions, including higher saturation densities and improved thermal stability of ssDNA monolayers in solutions containing divalent counterions. Surprisingly, we also find that the residual amount of divalent Ca2+ cations is unaffected by rinsing, but that monovalent K+ cations can be almost completely rinsed out in flowing deionized water. |