Thermodynamic analysis of conformational transitions in oligonucleotide complexes in presence of Na(+) and Mg(2+) ions, using "staggering zipper" model

Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface

Hybridization of homopolynucleotide poly(rC) adsorbed to the carbon nanotube surface with poly(rI) free in solution has been studied by absorption spectroscopy and molecular dynamics method. It was found that hybridization on the nanotube surface has a slow kinetics, the behavior of which differs essentially from fast hybridization of free polymers. The duplex obtained is characterized with the reduced thermostability and a lower hyperchromic coefficient than it was observed when the duplex was formed in the absence of the nanotube. These features point to the imperfectness in the structure of the duplex hybridized on the nanotube surface. Computer simulation showed that the strong interaction of nitrogen bases with the nanotube surface weakens significantly hybridization of two complementary oligomers, as the surface prevents the necessary conformational mobility of the polymer to be hybridized.