The Study of Biomolecule-Substrate Interactions by Single Molecule Force Spectroscopy and Brownian Dynamics Simulations.

摘要

Hybrids of biomolecules and nanomaterials have been identified as promising candidates in the development of novel therapeutics and electronic devices. Single stranded DNA (ssDNA)-bound Single-walled carbon nanotubes (SWCNTs) are of particular interest as they may be the key to solving the challenges that face the carbon nanotube separation technology and because of their potential application in bio-nanomedicine. The ability of ssDNA to form a stable hybrid with CNTs has been attributed to the structure and amphiphilic nature of this macromolecule, enabling the dispersion, sorting and patterned placement of nanotubes. Considering the significant role of ssDNA-CNTs in future technologies and the potential toxicity of such nanomaterials in biological systems, it is essential to gain a quantitative and fundamental understanding on the interactions that allow, weaken or prevent the formation of these hybrids. In this dissertation, we use both experimental and theoretical methods to systematically investigate the major characteristics of these interactions. The free energy of binding of ssDNA homopolymers to solvated carbon nanotubes is one of the key characteristics that determine the stability of such dispersions. We used single molecule force spectroscopy (SMFS), first on graphite and next on single walled carbon nanotubes, to probe and directly quantify the binding strength of ssDNA homopolymer oligomers to these substrates. The force resisting removal of DNA molecules from these surfaces shows characteristic steady-state force plateaus which were distinguishable for each DNA sequence. The free energy of binding per nucleotide for these oligomers on graphite were ranked as T >= A > G >= C (11.3 +/- 0.8 kT, 9.9 +/- 0.4 kT, 8.3 +/- 0.2 kT, and 7.5 +/- 0.8 kT, respectively). On SWCNTs, these interactions decreased in the following order: A > G > T > C, and their magnitude was much larger than on graphite (38.1 +/- 0.2; 33.9 +/- 0.1; 23.3 +/- 0.1; 17.1 +/- 0.1 kT, respectively). In addition to the binding strength of ssDNA nucleotide to surfaces, it is equally as important to understand the dynamics of these interactions. The force response of a simple chain-like polymeric molecule (representative of single stranded DNA) was studied using Brownian dynamics to shed light on these dynamics and the features that may be masked in SMFS experiments. Through simulations at slow peeling rates, our Brownian dynamics model confirmed the predictions of an equilibrium statistical thermodynamic model. Faster removal rates resulted in deviations from equilibrium which were dominated by a combination of Stokes (viscous) drag and a finite desorption rate of the monomeric units. Furthermore, the force probe's thermal fluctuations were shown to be affected by the spring constant of the contact mode AFM cantilever Consequently, this effect provided evidence on the source of disappearance for certain key features such as force spikes, associated with the desorption of individual links and predicted by the statistical thermodynamic model under displacement control, from SMFS experiments. In studying the elastic response of a freely jointed chain stretched in 2D and 3D, we obtained analytical expressions for two modes of stretching: i) when force is applied only to one end of the chain, and ii) when the applied force is distributed uniformly throughout the chain. By comparing, we confirmed that these expressions correctly predict the results obtained from our Brownian dynamics simulations as well as experimental results from the literature.