Galina O. Gladchenko

Adsorption of biopolymers on SWCNT: ordered poly(rC) and disordered poly(rI).

Polymer adsorption onto single-walled carbon nanotubes (SWCNTs) depends on its rigidity/flexibility. The adsorption properties of two related homopolynucleotides poly(rI) and poly(rC) but of different rigidities were compared, employing absorption spectroscopy and molecular dynamics simulation. It was shown that adsorption of the poor base stacked poly(rI) onto the nanotube is less effective than that of the strong base stacked poly(rC), the chain of which is of higher rigidity. Analysis of UV absorption spectra of polymer:nanotube suspension at heating until 90 °C, which leads to partial nanotube aggregation because of the weakly bound polymer sliding from the tube surface, revealed that the percent of precipitated nanotubes in suspension with poly(rI) is larger than that in suspension with poly(rC) (16% vs 7%). This fact indicates the higher stability of SWCNT:poly(rC) hybrid in comparison with SWCNT:poly(rI). Less effective adsorption of poly(rI) is confirmed with a weaker hypochromic effect of nanotubes covered with poly(rI) than with poly(rC), which originates from π-π stacking of nitrogen bases with the nanotube surface. Spontaneous adsorption of oligomers on the nanotube simulated by the molecular dynamics showed that oligomer r(I)25 has a weaker energy of binding to the carbon nanotube surface than r(C)25. The oligomer with ordered bases has a tendency to form the stretched conformation along the nanotube, which provides a higher binding energy, while more flexible r(I)25 forms the stable loop spaced away from the nanotube surface, the stability of which is strengthened with H-bonding between bases.

Studies of formation of bivalent copper complexes with native and denatured DNA

The formation of Cu2+ complexes with native and denatured DNA is studied by the methods of differential UV spectroscopy, CD spectroscopy, and viscometry. On ion binding to the bases of native DNA the latter transforms into a new conformation. This transition is accompanied with a sharp increase in UV absorption and a decrease in the intrinsic viscosity though the high degree of helicity persists. Possible sites of Cu2+ ion binding on DNA of various conformations are found along with corresponding constants of complex formation.

Interaction of divalent metal ions with poly(riboinosinic acid)

Methods of differential UV and visible spectroscopy are used to study the interaction of Mg 2+ , Ca 2+ , Ma 2+ and Cu 2+ ions with four (4 × 1), and single-stranded poly 1 is solutions with 1 mol.l -1 Na + . Up to concentrations of about 0.1 mol.l -1 Mt 2+ , Mg 3+ and Ca 2+ ions do not bind to hetereatoms of hypoxanthine of 4 × 1, Cu 5+ ions interact with N7 and/or N1 and possibly with O6 through the water molecule of the hydrate shell of the ion. It is likely that the interaction with O6 causes enolization of the hypoxanthine. N1 deprotonation and as a result, this leads to the melting of the four-stranded helix. In single-stranded chains, Cu 2+ ions induce the formation of compact particles which have the effective radii r e ≃ 100 A. The Ma 2+ -induced differential spectra are simalar to those observed in the presence of Cu 2+ ions but in the case of Mn 2+ they occur at concentrations about two orders of magnitude higher. In contrast to the positive cooperativity of the Cu 2+ binding to bases of single-stranded poly I, their interaction with 5 × 1 has the negative cooperativity.

Ni2+ ion effect on conformational transitions in triple helix of polyA-2polyU

Recently data were published on the participation of nucleic acids with non Watson-Crick pairing (of duplexes, triplexes and quadruplexes) in biological processes. It is of interest to study nucleic acid interactions with metal ions inducing mutagenesis and carcinogenesis.

Mg2+ ion effect on phase equilibrium in polyA·polyU and polyA·2polyU

Noncanonical structures of nucleic acids are involved in main biological reactions. To identify cell mechanisms of structural reconstructions in nucleic acids is a key problem of molecular biology. One of the factors having an influence on the stability of different structures is the ion environment. Na+ effects on structural transitions in such molecules as polyApolyU are well studied and phase diagrams are built [1]. The present work was aimed at building of the complete phase diagram for polyApolyU, polyA-2polyU complexes with Mg2+ at different ionic strengths.

Effects of divalent metal ions on secondary and tertiary structures of polyriboinosinic acid

Interest in noncanonical multichain helices (NMH) is aroused due to their taking part in biological processes. It is interesting to study effects of metal ions (Me2+) on NMH structures.

Peculiarities of Transition Metal Ion Interaction with DNA and Its Monomers

Distinctions in the interaction of divalent transition metal ions (Me) with nucleic acids (NA) are of interest in the connection with the determination of molecular mechanisms of the ion biological action. A new method is proposed to analyse forms of differential UV spectra (DUVS) of NA ’ metal complexes. The method determines the base atoms coordinating Me and thermodynamic parameters of their binding. Up to concentrations exceeding the polynucleotide one by 2 order of magnitude, Mn does not interact with bases of all nucleotides. The interaction is revealed only at the polymeric level (Table 1).