In this study we use AFM-based nanolithography technique to produce nanofeatures of the single strand DNA and LNA probe molecules which are prepared via thiolated nucleic acid self-assembled monolayers (SAMs) on gold substrates. The goal is to observe the topographic changes of the DNA film structures resulting from the formation of rigid double strand DNA when the target and probe DNAs bind together. The so-called hybridization depends strongly on the probe density on the substrate surface. To find the proper probe density for hybridization, we vary the concentration of the probe DNA and search for the optimal conditions for measuring the height changes of the nanofeatures. We also monitor the topographic changes of the DNA nanofeatures in the different target DNA concentrations as a function of time, and the binding isotherms are fitted with the Langmuir adsorption model to derive the equilibrium dissociation constant and maximum hybridization efficiency. In addition, we extend the nanoscale hybridization reaction detection to mismatched DNA:DNA and LNA:DNA hybridization, and observe that topographic change of mismatched hybridization is inconspicuous and rapidly reach equilibrium. The results reveal the apparent difference between the perfect match and mismatch conditions, and validate that this approach can be applied to differentiate the situations for both perfect match and mismatch cases, demonstrating its potentials in the gene chip technology.

Improving the identification ability of surfaced-immobilized nucleic acid probes for small size DNA or RNA targets, utilizing optical or electrochemical methods, has been the goal for the gene chip technology. This study focuses on new probe design for introducing hairpin structural features and locked nucleic acid modification. We use three kinds of probes (DNA-LN, DNA-HP and LNA-HP) to prepare recognition layers via self-assembly processes on a gold substrate, and utilize AFM-based nanolithography technique to produce nanofeatures to observe the stiffness changes of oligonucleotide chains resulting from the formation of rigid double stranded duplexes when target sequence hybridizes to the probe. We also monitor the topographic changes upon exposure to the single mismatched and non-complementary targets as a function of time. The results reveal LNA-HP probes exhibit the highest response to discriminating single-point mutation in the base sequence. In addition, we study the effects of salt concentration, reaction temperature and the small size on the hybridization efficiency.