Paper BI-WeA5
Hybridization with DNA Probes Bound to Gold by Adenine Nucleotides

Wednesday, October 17, 2007, 3:00 pm, Room 609

The surface density of immobilized nucleotide probes is a key variable in most applications of DNA-functionalized surfaces because the inter-molecular spacing has a strong impact on subsequent hybridization. In an earlier work, it was demonstrated that probe spacing can be controlled by exploiting the strong and preferential interaction between oligo(dA) and gold.¹ Using a model set of d(T_m-A_n) oligos, the lateral spacing between DNA molecules was found to be largely determined by the number of nucleotides, n, in the (dA) component; e.g. increasing the number of dA nucleotides in the sequence increased the spacing between probe strands. Here, we use both in situ (SPR) and ex situ (XPS) methods to demonstrate that the surface density of realistic DNA probe sequences can be controlled on gold by incorporating a d(T_m-A_n) ‘tail’ in the sequence. We find that surfaces functionalized in this fashion possess many desirable properties, including simplicity in fabrication, highly reproducible hybridization kinetics, and stability over multiple hybridization/melting cycles. The unique feature of our strategy is the relationship between the probe spacing and the length of the dA component in the probe. We find that an even wider range of probe-to-probe spacing can be achieved by co-immobilizing the probe DNA with unmodified oligo(dA), which acts as a lateral spacer. Altering either the length or mole fraction of this spacer systematically changes the probe DNA surface coverage, and thereby systematically modulates the hybridization response. Finally, we will discuss how hybridization with probes immobilized via our approach compares with DNA probes on gold prepared by more conventional strategies.

¹Opdahl et al., Proc. Nat. Acad. Sci., 104, 9, (2007).