title: Optimization of gold nanoparticle-based DNA detection for microarrays.
abstract: DNA microarrays are promising tools for fast and highly parallel DNA detection by means of fluorescence or gold nanoparticle labeling. However, substrate modification with silanes (as a prerequisite for capture DNA binding) often leads to inhomogeneous surfaces and/or nonspecific binding of the labeled DNA. We examined both different substrate cleaning and activating protocols and also different blocking strategies for optimizing the procedures, especially those for nanoparticle labeling. Contact angle measurements as well as fluorescence microscopy, atomic force microscopy (AFM), and a flatbed scanner were used to analyze the multiple-step process. Although the examined different cleaning and activating protocols resulted in considerably different contact angles, meaning different substrate wettability, silanization led to similar hydrophobic surfaces which could be revealed as smooth surfaces of about 2-4 nm roughness. The two examined silanes (3-glycidoxypropyltrimethoxysilane (GOPS) and 3-aminopropyltriethoxysilane (APTES)) differed in their DNA binding homogeneity, maximum signal intensities, and sensitivity. Nonspecific gold binding on APTES/PDC surfaces could be blocked by treatment in 3% bovine serum albumin (BSA).
authors.affiliation: Institute for Physical High Technology Jena, Jena, Germany. grit.festag@ipht-jena.de
authors.forename: Grit
authors.initials: G
authors.lastname: Festag
authors.forename: Andrea
authors.initials: A
authors.lastname: Steinbrück
authors.forename: Andreas
authors.initials: A
authors.lastname: Wolff
authors.forename: Andrea
authors.initials: A
authors.lastname: Csaki
authors.forename: Robert
authors.initials: R
authors.lastname: Möller
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Fritzsche
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000032:analysis*; D017931:DNA Primers; D006046:Gold / Q000737:chemistry*; D018625:Microscopy, Atomic Force; D008856:Microscopy, Fluorescence; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010316:Particle Size
chemical_list: D017931:DNA Primers; D006046:Gold; D004247:DNA