Although observation

of more cycles will provide higher accuracy in determining of the wrapping period, we believe that the precision achieved with three wrapping cycles observed in our experiments should suffice for http://www.selleckchem.com/CDK.html comparison with the modeling results and nanotube identification. Indeed, experimental height modulation profile in Figure 2(b) can be approximated by the sine wave, and the width of the peak in the fast-FT spectrum of sine wave spanning N periods (λ) is ~2λ/N Inhibitors,research,lifescience,medical at zero level. Due to noise in the measured profiles, any point above 90% of the maximum peak amplitude level can be considered as a center peak frequency. However, it will result in only ~0.12λ spread of the measured period around the actual value, which in our case is ~0.3nm. This error is much smaller than the difference between the wrapping periods for all the types of nanotubes present in the solution and should allow reliable

separation of hybrids containing nanotubes of different chiralities as described below. The nanotube edges influence the DNA-CNT binding and, thus, Inhibitors,research,lifescience,medical the wrapping geometry. This causes small coil-to-coil distance variations, Inhibitors,research,lifescience,medical so that the DNA wrapping is not perfectly aligned with the nanotube chiral vector. However, these variations are on the order of 0.1-0.2nm and fall well within the experimental error. Hence, they also can be neglected in the comparison of the modeled structure with the STM images. Using this procedure, the dependence of the frequency of occurrence of a particular period on its magnitude

for all hybrids in our images was extracted and is plotted in Figure 2(c). As can be seen, the characteristic period of the height variation along the CNT is 3.3nm and represents the coiling Inhibitors,research,lifescience,medical period of the DNA strand around CNT. Thus, our STM images reveal the DNA wrapping angle of ~63° and the most probable DNA coiling period of ~3.3nm. 5. Simulations Results and Discussion Inhibitors,research,lifescience,medical Previous molecular simulations [33] predict that short ssDNA strands can adopt a number of helical conformations when placed on a nanotube. The geometries observed by STM here suggest an existence of very specific stable structure with the DNA helical period of 3.3nm and the CYTH4 wrapping angle of ~63°. Our simulations of CNT-DNA hybrid constructed from the (6,5) tube and 20-mer ssDNA that was used in STM imaging have also resulted in a very stable configuration with the binding energy of −0.8eV per base, wrapping angles of ~63°, and wrapping period of 3.0–3.3nm, as shown in Figure 2(d). The optimized structure of the hybrid also confirms that the stable binding geometry of DNA nucleotides and CNT arises from the π-stacking interactions, which tend to align the nucleotide molecular plane parallel to the tube surface. For further examination of the stability of different CNT-DNA hybrid structures, we calculated the binding energy between various adsorbed ssDNA C-mers and G-mers and the (6,5) tube at different wrapping geometries, as shown in Figure 3.