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The general problem of designing force fields of nucleic acids for simulations is that the force field parameters for the bases are not able to reproduce (a) the dipole moments of the bases, (b) the base-base interactions, (c) the stacking interaction between the bases, and (d) the base-backbone interaction. In this work, the polarization effects of the base and backbone in DNA and RNA are taken into consideration with consistent atomic charges derived from first-principles in a vacuum. The atomic charges for DNA and RNA base and backbone are obtained by integrating the density of the electronic wave functions and the electrostatic potential at the atomic nuclei using the Coulomb interaction and the Dirac exchange and exchange-correlation potentials, respectively. The ability of the new atomic charges to determine the adsorption and conformational properties of a DNA and RNA sequence of a known sequence is tested.
Single-walled carbon nanotubes (SWNTs) have been evaluated for the production of nanocapsules that act as molecular hosts for human immunodeficiency virus (HIV-1). SWNTs are very effective for encapsulation of the viral protein gp160. Specific interactions between the nanotubes and gp160, and the resulting nanosized capsules, have been characterized using atomic force microscopy (AFM), and the nanoencapsulation of gp160 has been carried out using a cationic poly-L-lysine (PLL) and a neutral polyacrylamide (PAM) as the nanosizing agents. The combination of these two nanosizing agents in a single system proved to be very effective for the encapsulation of gp160 and was used for the determination of binding constants, encapsulation efficiencies, and number of binding sites. The binding constants of the nanotube-gp160 interactions were determined using the Langmuir adsorption model. The number of binding sites for the encapsulation of gp160 was estimated using the Bichromatic Electrophoresis technique. The nanocapsules obtained with the neutral PAM were found to be more stable than those obtained with the anionic PLL, probably due to a higher rigidity of the PAM capsules. The ability to control the size of the nanocapsules was also demonstrated, thus providing a new strategy for the production of nanoencapsulated active pharmaceutical ingredients.
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