We describe self-assembly of ssDNA brushes that exploits the intrinsic affinity of adenine nucleotides (dA) for gold surfaces. The grafting density and conformation of these brushes is deterministically controlled by the length of the anchoring dA sequences, even in the presence of thymine nucleotides (dT) FTIR ͉ gold ͉ immobilization ͉ oligonucleotides ͉ x-ray photoelectron spectroscopy T he properties of surfaces functionalized with ssDNA exhibit a remarkable richness that underlies the versatility of these surfaces in a wide range of applications. The ssDNA brushes described in this work offer unique properties for two types of applications: control of nanoscale self-assembly (1, 2) and design and operation of biosensors (3-8). In general, a critical attribute of a ssDNA-modified surface is efficient and reproducible hybridization with target DNA. Model studies using thiolated DNA probes have shown that efficient hybridization occurs when the spacing between immobilized DNA probes is large and the orientation of the probes is upright (4-11). Unfortunately, reproducible preparation of DNA films possessing both of these qualities remains challenging (12-14). For example, it is generally observed that when the grafting density is low (Ͻ10 13 cm Ϫ2 ), i.e., the spacing between probes is comparable to their length, DNA immobilizes in a flat conformation through nonspecific adsorption (9,15,16). This observation can be largely explained by conventional polyelectrolyte brush theory, which predicts that negatively charged DNA strands should only assume upright conformations in densely packed films, where repulsive interactions force the strands to extend away from the surface (7)..Surface passivation is a common strategy used to decouple the DNA conformation from grafting density. Passivation prevents nonspecific interactions between the surface and DNA or other biomolecules, which enables widely spaced DNA probes to maintain an upright orientation. In a common implementation of this strategy, films of thiol-anchored DNA can be exposed to a solution containing a competing molecule, such as mercaptohexanol (MCH), which displaces most of the DNA from the surface and forces the remaining DNA strands into an upright conformation (10,(17)(18)(19). Alternatively, grafting densities can be adjusted by coupling functionalized DNA to a bifunctional self-assembled monolayer (6).Our objective in this study is to control independently and deterministically both the conformation and grafting density of DNA. We realize this objective by introducing anchoring sequences of adenine nucleotides (dA), which in our previous work have been shown to have a high intrinsic affinity for gold surfaces (20). Here, the function of the adenine blocks [(dA)] extends, however, beyond simple anchoring: They preferentially bind to gold surfaces and block nearly all of the adsorption sites, preventing nonspecific binding of other sequences to these surfaces (an effect similar to that of using the MCH posttreatment or a bifunctional self-assembled mon...

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We report the successful application of SFG to detect segregation of end groups on polymer surfaces. Two groups of polymer samples are studied: one is polyurethane with different surface-modified end groups, the other is poly(ethylene glycol) (PEG) with different end groups. For each group of polymers, both hydrophobic and hydrophilic end groups are chosen. With the surface sensitivity of SFG, we have found that hydrophobic end groups [e.g., methoxy on PEG or poly(dimethylsiloxane) (PDMS) on polyurethane] tend to segregate to the polymer surface in air. However, the hydrophilic end groups (e.g., hydroxyl group on PEG or PEG on polyurethane) remain in the bulk so that the surfaces that are exposed to air are covered by the polymer backbones. Although contact-angle measurements and XPS results can demonstrate that polymer surfaces indeed have been modified by different end groups, only SFG can show the surface structure at the molecular level.

We have studied the formation of self-assembled monolayers (SAMs) of n-alkanethiols on platinum thin films using X-ray photoelectron spectroscopy (XPS), reflection-absorption infrared spectroscopy (RAIRS), spectroscopic ellipsometry (SE), and contact angle (CA) measurements. Specifically, SAMs of 1-hexanethiol, 1-dodecanethiol, and 1-octadecanethiol were grown on polycrystalline Pt films, and the effects of Pt surface preparation, deposition conditions, and solvent treatments on the initial quality and stability of the monolayer in air were investigated. The SAMs prepared under ambient conditions on piranha-cleaned and UV/ozone-cleaned substrates were compared to monolayers formed on template-stripped Pt in an inert atmosphere. We found that alkanethiols deposited from 1 mM ethanolic solutions on piranha-cleaned Pt formed densely packed monolayers in which alkyl chains were oriented close to the surface normal. Stored in the laboratory ambient, these monolayers were unchanged over about 1 week but were largely oxidized in about 1 month. No evidence was found of molecules being weakly bound within the monolayer or having undergone C-S bond scission; however, three distinct sulfur states were observed for all samples in the XPS of the S 2p region. The lowest-and highest-binding-energy components are assigned to alkylthiolate and partially oxidized alkylthiolate species, respectively. The remaining S 2p component (approximately one-third of the sulfur layer), intermediate in binding energy between the other two components, is attributed to a chemisorbed species with a S binding configuration distinct from the majority alkylthiolate: for example, S bound to Pt bound to O, S with a different Pt coordination number, or S in an adsorbed disulfide.

Quantitative and reproducible data can be obtained from surface-based DNA sensors if variations in the conformation and surface density of immobilized single-stranded DNA capture probes are minimized. Both the conformation and surface density can be independently and deterministically controlled by taking advantage of the preferential adsorption of adenine nucleotides (dA) on gold, as previously demonstrated using a model system in Opdahl, A.; Petrovykh, D. Y.; Kimura-Suda, H.; Tarlov, M. J.; Whitman, L. J. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 9-14. Here, we describe the immobilization and subsequent hybridization properties of a 15-nucleotide DNA probe sequence that has additional m adenine nucleotides, (dA)(m), at the 5' end. Quantitative analysis of immobilization and hybridization for these probes indicates that the (dA)(m) block preferentially adsorbs on gold, forcing the probe portion of the strand to adopt an upright conformation suited for efficient hybridization. In addition, a wide range of probe-to-probe lateral spacing can be achieved by coimmobilizing the probe DNA with a lateral spacer, a strand of k adenine nucleotides, (dA)(k). Altering either the length or relative concentration of the (dA)(k) spacers added during probe immobilization controls the average surface density of probes; the density of probes, in turn, systematically modulates their hybridization with solution targets.

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The structure and stability of single- and double-stranded DNA hybrids immobilized on gold are strongly affected by nucleotide-surface interactions. To systematically analyze the effects of these interactions, a set of model DNA hybrids was prepared in conformations that ranged from end-tethered double-stranded to directly adsorbed single-stranded (hairpins) and characterized by surface plasmon resonance (SPR) imaging, X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The stabilities of these hybrids were evaluated by exposure to a series of stringency rinses in solutions of successively lower ionic strength and by competitive hybridization experiments. In all cases, directly adsorbed DNA hybrids are found to be significantly less stable than either free or end-tethered hybrids. The surface-induced weakening and the associated asymmetry in hybridization responses of the two strands forming hairpin stems are most pronounced for single-stranded hairpins containing blocks of m adenine (A) nucleotides and n thymine (T) nucleotides, which have high and low affinity for gold surfaces, respectively. The results allow a qualitative scale of relative stabilities to be developed for DNA hybrids on surfaces. Additionally, the results suggest a route for selectively weakening portions of immobilized DNA hybrids and for introducing asymmetric hybridization responses by using sequence design to control nucleotide-surface interactions--a strategy that may be used in advanced biosensors and in switches or other active elements in DNA-based nanotechnology.

The surface composition and surface chain conformation of a series of random aspecific poly(ethylene-copropylene) rubber copolymers (aEPR) was quantified by sum frequency generation surface vibrational spectroscopy (SFG). All of the copolymers are found to preferentially orient side-branch methyl groups out of the surface. As the ethylene content of the copolymer increases, the number of methyl groups contributing to the sum frequency signal decreases. However, the percentage of methyl groups oriented out of the surface, relative to the bulk concentration of methyl groups, increases. This surface excess of oriented methyl groups is proposed to be a result of decreased steric hindrances between adjacent methyl groups in ethylene-rich copolymers. Additionally, analysis of the CH 2 bands in the SFG spectra suggests that the CH 2 units at the surface become more oriented toward the surface normal and adopt a trans configuration as the ethylene content increases.