silicon and cyanine-dye-3

DNA origami nanostructures are a versatile tool to arrange metal nanostructures and other chemical entities with nanometer precision. In this way gold nanoparticle dimers with defined distance can be constructed, which can be exploited as novel substrates for surface enhanced Raman scattering (SERS). We have optimized the size, composition and arrangement of Au/Ag nanoparticles to create intense SERS hot spots, with Raman enhancement up to 10(10), which is sufficient to detect single molecules by Raman scattering. This is demonstrated using single dye molecules (TAMRA and Cy3) placed into the center of the nanoparticle dimers. In conjunction with the DNA origami nanostructures novel SERS substrates are created, which can in the future be applied to the SERS analysis of more complex biomolecular targets, whose position and conformation within the SERS hot spot can be precisely controlled.

Topics: Carbocyanines; Dimerization; DNA; DNA, Single-Stranded; Gold; Metal Nanoparticles; Microscopy, Atomic Force; Microscopy, Electron, Scanning; Nanotechnology; Nucleic Acid Hybridization; Rhodamines; Scattering, Radiation; Silicon; Silver; Spectrum Analysis, Raman

We demonstrated the surface functionalization of a highly three-dimensional, superhydrophilic wicking substrate using light to immobilize functional biomolecules for sensor or microarray applications. We showed here that the three-dimensional substrate was compatible with photo-attachment and the performance of functionalization was greatly improved due to both increased surface capacity and reduced substrate reflectivity. In addition, photo-attachment circumvents the problems induced by wicking effect that was typically encountered on superhydrophilic three-dimensional substrates, thus reducing the difficulty of producing miniaturized sites on such substrate. We have investigated various aspects of photo-attachment process on the nanowire substrate, including the role of different buffers, the effect of wavelength as well as how changing probe structure may affect the functionalization process. We demonstrated that substrate fabrication and functionalization can be achieved with processes compatible with microelectronics processes, hence reducing the cost of array fabrication. Such functionalization method coupled with the high capacity surface makes the substrate an ideal candidate for sensor or microarray for sensitive detection of target analytes.

Topics: Carbocyanines; DNA Probes; Immobilized Nucleic Acids; Microarray Analysis; MicroRNAs; Miniaturization; Nanowires; Nucleic Acid Hybridization; Nucleic Acids; Silicon; Surface Properties; Ultraviolet Rays

Reliable and efficient identification of DNA is a major goal in on-site diagnostics. One dimensional nanostructures like nanowires (NW) represent potential sensor structures due to their extreme surface-to-bulk ratio, enabling enhanced biomolecule binding which results in optimal signals. While silicon NW are already well studied, NW made from other materials with promising properties like ZnO are not yet established as NW sensor material for bioanalytics. Here we demonstrate the DNA functionalization of ZnO NW even at the single NW level and their successful application in a DNA hybridization assay.

Topics: Carbocyanines; DNA; Fluorescent Dyes; Immobilized Nucleic Acids; Nanotechnology; Nanowires; Nucleic Acid Hybridization; Optical Phenomena; Silicon; Transducers; Zinc Oxide

Cellular patterning on silicon platforms is the basis for development of integrated cell-based biosensing devices, for which long-term cell selectivity and biostability remain a major challenge. We report the development of a silicon-based platform in a metal-insulator format capable of producing uniform and biostable cell patterns with long-term cell selectivity. Substrates patterned with arrays of gold electrodes were surface-engineered such that the electrodes were activated with fibronectin to mediate cell attachment and the silicon oxide background was passivated with PEG to resist protein adsorption and cell adhesion. Three types of oxide surfaces, i.e., native oxide, dry thermally grown oxide, and wet thermally grown oxide, were produced to illustrate the effect of oxide state of the surface on long-term cell selectivity. Results indicated that the cell selectivity over time differed dramatically among three patterned platforms and the best cell selectivity was found on the dry oxide surface for up to 10 days. Surface analysis results suggested that this enhancement in cell selectivity may be related to the presence of additional, more active oxide states on the dry oxide surface supporting the stability of PEG films and effectively suppressing the cell adhesion. This research offers a new strategy for development of stable and uniform cell-patterned surfaces, which is versatile for immobilization of silane-based chemicals for preparation of biostable interfaces.

Topics: Animals; Biosensing Techniques; Carbocyanines; Cell Line; Cytological Techniques; Fibronectins; Gold; Macrophages; Mice; Microscopy, Fluorescence; Oxidation-Reduction; Polyethylene Glycols; Silicon; Silicon Dioxide; Surface Properties

We demonstrate apertureless near-field microscopy of single molecules at sub-10 nm resolution. With a novel phase filter, near-field images of single organic fluorophores were obtained with approximately sixfold improvement in the signal-to-noise ratio. The improvement allowed pairs of molecules separated by approximately 15 nm to be reliably and repeatedly resolved, thus demonstrating the first true Rayleigh resolution test for near-field images of single molecules. The potential of this technique for biological applications was demonstrated with an experiment that measured the helical rise of A-form DNA.

Topics: Algorithms; Carbocyanines; DNA, A-Form; Fluorescent Dyes; Microscopy, Atomic Force; Microscopy, Confocal; Microscopy, Fluorescence; Nucleic Acid Conformation; Silicon