Controlled and Efficient Hybridization Achieved with DNA Probes Immobilized Solely through Preferential DNA-Substrate Interactions

Quantitatively correlating the response of DNA sensors to clinically and biologically significant sample abundances requires optimizing the reproducibility of hybridization between DNA targets and surface-bound DNA probes. 1,2 Although gold surfaces are not used in commercial fluorescence-based DNA arrays, gold offers many useful properties as a model substrate 3 and has been successfully used in systematic studies of the interactions governing DNA hybridization near interfaces. 4-8 The hybridization behavior of surface-immobilized DNA probes strongly depends on the probe conformation and on the lateral spacing between adjacent probes. Hybridization is generally enhanced for DNA probes that extend away from a surface, in part because steric hindrance is lower for such brushlike probes than for DNA directly adsorbed on gold. At surface densities e5 × 10 12 cm -2 , typical probe sequences (15-30 nucleotides) can hybridize with efficiencies >60%, 7-10 but at probe densities >1 × 10 13 cm -2 hybridization efficiency is often reduced because of increased electrostatic repulsion and steric constraints. 11-13 Surfaces with DNA probes in upright conformations can be prepared following a number of strategies, including adsorption via a thiol incorporated at one end (DNA-SH) or coupling DNA probes to bifunctional monolayers. [4][5][6][7][8][14][15][16][17][18] Preparing DNA probes * To whom correspondence should be addressed. E-mail: opdahl

Influence of Attachment Strategy on the Thermal Stability of Hybridized DNA on Gold Surfaces

The thermal stabilities of double-stranded DNA hybrids immobilized on gold surfaces are shown to be significantly affected by the conformation of the hybrid. To analyze this behavior, DNA probes were immobilized using attachment strategies where the nucleotides within the strand had varying levels of interactions with the gold substrate. The abilities of these probes to form double-stranded hybrids with solution DNA targets were evaluated by surface plasmon resonance (SPR) over a temperature range 25–60 °C. The measurements were used to construct thermal stability profiles for hybrids in each conformation. We observe that DNA hybrids formed with probe strands that interact extensively with the gold surface have stability profiles that are shifted lower by 5–10 °C compared to hybrids formed with end-tethered probes that have fewer interactions with the surface. The results provide an understanding of the experimental conditions in which these weaker DNA hybrids can form and show the additional complexity of evaluating denaturation profiles generated from DNA on surfaces

Temperature Gradient Approach for Rapidly Assessing Sensor Binding Kinetics and Thermodynamics

We report a highly resolved approach for quantitatively measuring the temperature dependence of molecular binding in a sensor format. The method is based on surface plasmon resonance (SPR) imaging measurements made across a spatial temperature gradient. Simultaneous recording of sensor response over the range of temperatures spanned by the gradient avoids many of the complications that arise in the analysis of SPR measurements where temperature is varied. In addition to simplifying quantitative analysis of binding interactions, the method allows the temperature dependence of binding to be monitored as a function of time, and provides a straightforward route for calibrating how temperature varies across the gradient. Using DNA hybridization as an example, we show how the gradient approach can be used to measure the temperature dependence of binding kinetics and thermodynamics (e.g., melt/denaturation profile) in a single experiment

Effect of Probe–Probe Distance on the Stability of DNA Hybrids on Surfaces

We have used temperature gradient surface plasmon resonance (SPR) measurements to quantitatively evaluate how the stability of different types of hybrids formed with DNA probes on surfaces is affected by probe spacing. SPR sensors with different average surface densities of probes were prepared by coadsorbing probes with lateral spacers strands comprised of phosphorothioated adenine nucleotides (A15*). Increasing the fraction of A15* spacers in the immobilization solution results in larger distances between probes on the sensor, determined here using a combination of SPR and X-ray photoelectron spectroscopy (XPS) measurements. The hybridization activities of probes were simultaneously measured over a temperature range that spanned the denaturation temperature (<i>T</i>_m) of hybrids by applying a spatial temperature gradient across the sensor surface. The resulting temperature profiles of hybridization activity show how the stability of hybrids increases as either the distance between probes or the ionic strength of the hybridization buffer increase. Additionally, hybridization activity profiles sharpen as the spacing between probes increases, indicating more homogeneous hybridization behavior of probes. The results provide quantitative experimental data for testing theoretical models of stability, supporting models that account for both repulsive interactions between DNA strands and local variability in probe surface density

Synthesis and structural characterization of glucopyranosylamide films on gold

Self-assembled monolayers (SAMs) of glucose derivatives on gold have been prepared from α- and β-glucopyranosylamide derivatives. The glucosyl conjugates were synthesized stereoselectively via the in situ generation of glucosyl isoxazolines followed by treatment with thiopyridyl esters. The resulting film structures were characterized by atomic force microscopy, reflection Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy. The experimental data indicated that α- or β-linked glucopyranosylamide derivatives with free hydroxyl groups attach to gold via the thiol linker. Both derivatives form monolayer films with high packing densities-comparable to those typically observed for alkanethiol monolayers on gold. Acetate analogues of these conjugates do not form SAMs on gold; they form multilayered films under identical deposition conditions. © 2007 American Chemical Society