Prashant D. Sawant

Microbeads on microposts: an inverted architecture for bead microarrays.

The rapid development of genomics and proteomics requires accelerated improvement of the microarrays density, multiplexing, readout capabilities and cost-effectiveness. The bead arrays are increasingly attractive because of their self-assembly-based fabrication, which alleviates many problems of top-down microfabrication. Here we present a simple, reliable, robust and modular technique for the fabrication of bead microarrays, which combines the directed assembling of beads in microstructures and PDMS-based replica molding. The beads are first self-assembled in pyramidal microwells fabricated by anisotropic etching of silicon substrates, then transferred on the apex of PDMS pyramids that replicate the silicon microstructures. The arrays are chemically and biochemically robust; they are spatially addressable and have the potential for being informationally addressable; and they appear to offer better readout capabilities than the classical microarrays.

Line and two-dimensional fractal analysis of micrographs obtained by atomic force microscopy of surface-immobilized oligonucleotide nano-aggregates

This study reports on the evaluation of the nanotopographies of DNA functionalized polymer surfaces, i.e., cyclo-olefine copolymer (COC) and polycarbonate (PC) using line, “Zmax” and two dimensional fractal dimension methods, i.e., power spectrum density algorithm (PSDA) and perimeter-area relationship (PAR), applied to atomic force microscopy (AFM) scans. A decrease in the fractal dimension after the immobilization of oligonucleotides suggests the prevalence of a vertical assembly of oligonucleotides, more significantly on COC than on PC.

Hierarchy of DNA immobilization and hybridization on poly-L-lysine: An atomic force microscopy study

Atomic force microscopy is used to analyze the immobilization of single-stranded DNA (ssDNA) on poly-L-lysine (PL)-coated glass and subsequent hybridization with complementary DNA (dsDNA). 2D fractal analysis (power spectrum density algorithm (PSDA)) and line analysis methods are used to characterize the vertical aggregation of ssDNA/dsDNA. The nanodefects on the PL layer could be responsible for the vertical aggregation of DNA. The line analysis suggests that approximately two layers of ssDNA are adsorbed, stacked vertically. The PSDA is useful in understanding the direction of aggregation in addition to understanding the growth mechanism. Fractal dimension values are between 2 and 3, suggesting that the growth mechanism may obey the diffusion-limited aggregation (DLA) model.

Microablation of gold nanolayers by direct write lithography

The laser ablation is widely used for the formation of metal nanoparticles, nanorods, nanodisks, nano-networks and polymeric microchannels. This paper reviews the results obtained when using of the microablation of the gold layers that are tens of nanometer think deposited on various transparent surfaces, such as Poly(tert-butyl methacryalate), Poly(methyl methacrylate) -PMMA, Polydioxymethyl siloxane, PDMS, and glass, with a low power laser (low fluences of 4-500 ?J/cm2, 337nm wavelength and 4ns pulses). The microablation results in the preferential formation of gold wire-like nanostructures at the edges and across the ablated channels on PMMA and PTBMA; and of gold nanoparticles on glass and PDMS. This contrasting behavior is explained by the presence of gas-generating pyrolysis on PMMA or PTBMA as opposed to lack of it on glass and PDMS.

AFM analysis of the formation of DNA aggregates on polymeric biochips

The demand for polymer-based DNA microarrays will increase because of their cost-effectiveness, biocompatibility and easy processing. However not all polymers are ideal substrates because of different chemical interactions of polymeric substrates with the DNA molecules. Results from AFM analysis of DNA immobilised on polymeric surfaces are evaluated using fractality, Gaussian distribution and lateral force imaging. It has been found that the nanosize defects in the substrate, such as poly-l-lysine, plays an important role in the growth of DNA aggregates in a vertical direction, whereas the covalent binding of DNA molecules on NHS-functionalised cyclo-olefin copolymer leads to the lateral growth of DNA aggregates.

An AFM study of the hierarchical DNA immobilization/hybridization processes on surfaces

The immobilization and hybridization processes of DNA strands on poly-l-lysine (PL) covered surfaces have been studied using the atomic force microscopy (AFM) in a topographic mode. The statistical analysis of topographic surfaces showed an increase in the Z-threshold with additions of single strand DNA (ssDNA) and the complimentary DNA (ccDNA). Also no drastic change of statistical fractal dimension (slope of the log-log perimeter-area plot) is observed when comparing the PL-surfaces coated with ssDNA and ccDNA. These two results suggest that ssDNA strands are successfully immobilized and spatially hybridized with ccDNA on the PL surface and the growth of hybridized ccDNA occurs mainly in the vertical dimension. The methods described here are good candidates for the detection of DNA hybridization, especially in the context of DNA nanoarrays.