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We demonstrate here a novel single-molecule, label-free bioanalytical system capable of sensing the presence of specific ssDNA oligomer sequences and proteins with high selectivity and sensitivity. An ssDNA concentration of 1 nM and a Lyz concentration of 0.65 nM could be detected.

We report here a systematic investigation of the interactions between two heteropolymer DNA single-strands (ssDNA) and graphite surfaces using AFM-based single-molecule force spectroscopy (SMFS). For this purpose, force-displacement (FD) curves are recorded by peeling single-molecule ssDNA from graphite. We find that the unbinding forces are affected both by the DNA sequences and the ionic strength of the liquid environment. In particular, the unbinding force decreases with the increase of ionic strength. Dynamic force measurements indicate that the unbinding force increases nonlinearly with the logarithm of the applied loading rate. The force data at different loading rates can be fitted with a recently developed single-barrier adsorption model, which is used here as a mean of quantifying the differences in the adsorption between different sequences. In addition, we investigate the effect of DNA hybridization and the presence of mismatch pairing defects and find that flawless hybridization to a complementary oligomer significantly decreases the unbinding force but mismatched hybridization has no obvious effect on it. These results can help optimize a recently envisaged SMFS-based biosensing technology for label-free DNA detection.

We introduce a novel technique for an initial identification of peptide sequences that specifically bind to material surfaces based on the matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-ToF MS) depletion method. The technique relies upon time-resolved, sensitive measurements of the MALDI-ToF MS peak signals acquired from a solution containing several peptides placed in contact with an inorganic surface, in our case amorphous SiO2. Large errors intrinsic in the MALDI-ToF MS spectral analysis and uncertainties arising from the adsorption behaviour of peptide mixtures limit the predictive power of the method. However, when combined with other characterisation and modelling techniques, such as High-Performance Liquid Chromatography (HPLC), Atomic Force Microscopy (AFM), Quartz Crystal Microbalance with Dissipation (QCM-D) and Molecular Dynamics (MD), it can be used as a guide to identify novel material-binding peptide sequences, such as TPGSR for SiO2. The strategy presented in this work may have an impact on the design and synthesis of novel hybrid biomaterials based on the biomolecular recognition of inorganic surfaces

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