DNA---carbon nanotube interactions

Hybrids of biomolecules and nanomaterials offer unique opportunities for the development of novel therapies and device applications. A system of special interest is the hybrid of ssDNA and CNT's (DNA-CNT). DNA-CNT hybrids have several potential applications in medicine and materials technology. ssDNA forms a stable hybrid with CNTs, enabling their dispersion, sorting and patterned placement. Given the central role of DNA in biology and CNT in nanomaterials engineering, understanding the DNA-CNT hybrid structure can have important implications. The manipulation of the hybrid and its mechanics depend on the hybrid structure and the interactions between DNA and CNT. Using both experimental and theoretical methods, this thesis addresses the questions about the structure and binding thermodynamics of DNA-CNT hybrids.;Several physical factors governing the hybrid formation are identified. First detailed molecular dynamics study of DNA-CNT hybrid formed between a CNT and single homopolymer ssDNA strands are reported. Compared to large stacking interaction between the base and CNT, the barrier for lateral movement is small which makes the CNT surface frictionless. Ignoring the hydrogen bonding interactions, base-CNT adhesion and the electrostatic repulsion due to charged backbone are the main interactions. A simple model predicts a tightly wrapped structure.;Using graphite as a model surface for CNT, the adhesion of short ssDNA chains with graphite surface is directly measured using single molecule force spectroscopy. Force traces during retraction of AFM tip chemically modified with oligonucleotides from graphite substrate displayed characteristic plateaus with abrupt force jumps interpreted as steady peeling punctuated by complete detachment of one or more molecules. The measured peeling forces are 85.3 pN for polythymine, 60.8 pN for polycytosine and 74.6 pN for polyadenine, and the corresponding monomer binding energies calculated using a statistical thermodynamics model are 11.5, 8.3 and 9.7 kBT. The model predicts the DNA chain to peel at steady force under force control and link-by-link under displacement control. This suggests that under displacement control with a sufficiently stiff loading system it might be possible to extract sequence information by force spectroscopy.;Novel ordered DNA structures on graphite and CNT, analogous to protein beta-sheet and beta-barrels are proposed, consistent with several experiments. Ordered DNA structures are proposed as the structural basis for CNT recognition enabling chromatographic purification of semiconducting CNTs. The anomalously large adhesion during peeling of special sequences like (TATT)n from graphite in force spectroscopy experiments suggest the formation of stable secondary structures that peel as a whole. The (charge density, mass ratio) of the ordered DNA-CNT models are (5.8, 1.76) for (6,5) CNT and (6.2, 1.70) for (7,5) CNT, in good agreement with the values obtained via capillary electrophoresis.