For the fixed DNA geometries, when a few DNA bases at the ends are not free to move with other atoms of the systems during geometry optimization, the homogeneity of wrapping

angles improves significantly; see Figure 3 (left panel). Overall, the deviation from a mean value of wrapping angle is about 10°–15° for the PKI-587 purchase structures with fixed ends and up to 20°–30° for structures with free ends. Figure 4 shows the binding energy of the DNA and the (6,5) SWNT as a function of the average wrapping angle. The minimum of the curve indicates the most stable Inhibitors,research,lifescience,medical hybrid configuration with the strongest interaction between the tube surface and the DNA strand. For all C-mers, a well-defined minimum is found in the range of 58°–63°; these wrapping angles correlate well with the chiral angle of the (6,5) Inhibitors,research,lifescience,medical tube. For the G-mer, the minimum is slightly shifted towards smaller angles of 50°–60°. For all hybrids we considered, the energy barrier around the minimum is about 0.2-0.3eV, which is significantly higher than thermal fluctuation energies.

The CNT-DNA interactions are also very substantial (−0.6eV and −0.8eV) implying very stable hybrid configurations for wrapping angles of 50°–63°. Thus, we conclude that hybrids with DNA wrapped in correlation with the (6,5) chirality of nanotube have extremely stable configurations. For these structures, ssDNA is unlikely Inhibitors,research,lifescience,medical to be detached from the tube because of external perturbations, such as ambient thermal vibrations, solvent effects, and exchanges with blood serum. All these observations point to the utility of DNA-functionalized Inhibitors,research,lifescience,medical CNT for medicinal purposes. Figure 4 Variation of the binding energy of the CNT-DNA hybrids with the DNA wrapping angle. Inhibitors,research,lifescience,medical The solid lines correspond to hybrid configurations with fixed ends, that is, where the end bases of the DNA molecule are fixed and all other atoms of the hybrid system … The smaller the wrapping angle of

C-mers, the larger the energy, reflecting much weaker interaction of cytosine-oligomers with the CNT for these geometries. In contrast, G-mers provide very stable configurations not only at 50°–60° but also at small wrapping found angles of 10°–20°. Interestingly, not all guanine molecules are oriented parallel to the tube surface at small wrapping angles, as observed for cytosine-oligomers: a few guanine bases have nearly normal orientation to the tube surface and form the π–π stacking with each other. This behavior most likely originates from a larger size of guanines compared to cytosines, which favors such interactions. The difference between C-mer and G-mer optimal wrapping angles, at which the most stable hybrid conformations occur, may explain a previously observed difference in stability of CNT-DNA hybrids with respect to the chemical structure/sequence of the adsorbed DNA.