Direct force measurements on peeling heteropolymer ssDNA from a graphite surface using single-molecule force spectroscopy

Abstract

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.