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.
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.