Hierarchy of DNA immobilization and hybridization on poly-L-lysine using an atomic force microscopy study

The atomic force microscopy has been used to analyze the immobilization of single stranded DNA on poly-L-lysine-coated glass and subsequent hybridization with complimentary DNA with the Z-threshold parameter and fractal analysis methods. The poly-L-lysine layer, which has a thickness of approximately 7 nm, presents nano-defects that could be critical for DNA immobilization by acting as a nucleation sites for ssDNA and subsequently for dsDNA aggregates. The Z-threshold for the dsDNA aggregates is much larger than for ssDNA, but the statistical fractal dimension is very similar, suggesting a conformal increase of the dimensions of the dsDNA aggregates mainly in the Z-direction, due to an effective ssDNA-ccDNA molecular recognition. This study demonstrates the use of fractal analysis in conjunction with the distribution of heights to evaluate the efficiency of DNA-DNA molecular recognition on surfaces and the impact of nanodefects.