Nature of Interactions between Single-Stranded DNA Molecules and Graphene Substrate through Atomic Force Microscope

During this thesis project research, there were collected experimental data regarding interactions of individual DNA molecules with monolayer graphene and develop a breakthrough model to explain data. Moreover, there were investigated the fundamental interactions involved when individual single-stranded DNA molecules and underlying graphene surface are in contact and when they mutually detach. For that purpose, it was used Single-Molecule Force Spectroscopy (SMFS) with the help Atomic Force Microscope (AFM). Force vs distance curves have been collected inside the liquid environment, which shows characteristic force plateaus once individual molecules are peeled off from the surface. Plateaus that correspond to desorption of last individual DNA molecule near AFM tip apex are statistically analyzed after experiments, with our data collected into histograms which are fitted with appropriate Gaussian curves. ssDNA chains employed for analysis have been 100 nucleotides long A-homopolymers (ade-nine), C-homopolymers (cytosine) and T-homopolymers (thymine), forces are measured in the temperature range 5◦C - 35◦C, and for different tip velocities of approach and retraction of AFM probe 200nm/s−1500nm/s. Aim of our experiment is to understand the main mechanisms which play a key role in the total interaction between DNA and monolayer graphene surface. Our analysis will show that dominant contributions are hydrophobic and pi stacking interactions, with a negligible electrostatic contribution, and we will provide their experimental values. From the measurement of dependence of forces on the velocity of the tip during approach/retraction, we infer that detachment of individual molecules is an equilibrium process, which simplifies the construction of a model to describe experimental data. By studying the temperature dependence of total interaction, and developing a theoretical model which uses into account contact angle measurements and use of quantity which is called interfacial free energy, we directly connect slopes of experimental fit lines with the presence of hydrophobic interactions in the system, while intersects on y-axis give us values of van der Walls force inside the system.