Independent control of grafting density and conformation of single-stranded DNA brushes

Abstract

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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