| AVS 57th International Symposium & Exhibition | |
| Biomaterial Interfaces | Wednesday Sessions |
| Session BI1-WeM |
| Session: | Biomolecules at Interfaces |
| Presenter: | N. Vandencasteele, University of Washington |
| Authors: | N. Vandencasteele, University of Washington L. Árnadóttir, University of Washington J.E. Baio, University of Washington T.M. Weidner, University of Washington L.J. Gamble, University of Washington |
| Correspondent: | Click to Email |
The hybridization efficiency of DNA microarrays and biosensors is determined in part by variables such as the density and orientation of the single stranded DNA oligomers used to build the devices. In order to better understand the chemistry on the microarray surfaces, and therefore improve their response, we study model surfaces of DNA adsorbed on gold with x-ray photoelectron spectroscopy (XPS), near-edge x-ray absorption fine structure (NEXAFS) spectroscopy and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to characterize the surface order and structure. We previously showed that varying the amount of diluent molecule, and thus the probe density, affects the hybridization efficiency of a 20mer thiolated single stranded DNA probe and the target.1,2 In this study we compare the density and orientation of a 40mer single-stranded thiolated DNA (HS-ss-DNA), when varying amounts of the diluent molecule 11-mercapto-1-undecanol (MCU) are adsorbed. DNA is detected on the surface using XPS (N1s and P2p peaks) and ToF-SIMS analysis. ToF-SIMS results for various backfill times and various backfilling media are compared using PCA analysis. In the first set of experiments the MCU backfill reaction takes place in water (ultra pure 18 MΩ), in the second set of experiment it takes place in sodium Tris EDTA buffer solution (STE). We showed that when the co-adsorption reaction is done with a solution of MCU in water, the amount of MCU that incorporates into the surface saturates at 18h and the amount of DNA on the surface remains relatively constant. When the same experiment is carried out using a MCU solution in STE buffer the MCU binding removes the surface bound DNA and all of the HS-ss-DNA is removed from the surface after 2h, suggesting a better hydration of the DNA in the STE medium. The improved hydration of the DNA increases it’s mobility in the solution allowing an easier access of the MCU to the gold surface. Angle dependent NEXAFS spectra taken for DNA layers after different MCU backfill times in water showed the highest degree of orientational order after a 30 min MCU backfilling step. The data also indicate that the DNA nucleotide base rings are ordered parallel to the surface. Hybridization efficiencies of the 40 mer DNA layer with various densities will be compared with surface plasmon resonance (SPR).
(1) Gong, P.; Lee, C.-Y.; Gamble, L. J.; Castner, D. G.; Grainger, D. W. Analytical Chemistry 2006, 78, 3326-3334.
(2) Lee, C.-Y.; Gong, P.; Harbers, G. M.; Grainger, D. W.; Castner, D. G.; Gamble, L. J. Analytical Chemistry 2006, 78, 3316-3325.