The photosensitive azobenzene-containing surfactant C 4 -Azo-OC 6 TMAB is a promising agent for reversible DNA packaging in a solution. The simulation of the trans-isomer surfactant organization into associates in a solution with and without salt as well as its binding to DNA at different NaCl concentrations was carried out by molecular dynamics. Experimental data obtained by spectral and hydrodynamic methods were used to verify the results of simulation. It was shown that head-to-tail aggregates with close to antiparallel orientation of surfactant molecules were formed at certain NaCl and surfactant concentrations (below critical micelle concentration). Such aggregates have two positively charged ends, and therefore, they can be attracted to negatively charged DNA phosphates far located along the chain, as well as those that belong to different molecules. This contributes to the formation of intermolecular DNA–DNA contacts, and this way, the experimentally observed precipitation of DNA can be explained.

The DNA interaction with cis-isomers of photosensitive azobenzenecontaining surfactants was studied by both experimental methods and computer simulation. It was shown that before the organization of micelles, such surfactants in the cis-conformation form associates of only a single type with a disordered orientation of molecules. In contrast, for trans-isomers, there exist two types of associates with headto-head or head-to-tail orientations of molecules in dependence on salt concentration in a solution. The comparison of cis-and trans-isomer binding to DNA and the influence of salt concentration on the formation of their complexes with DNA were studied. It was shown that cis-isomers interact with phosphate groups of DNA and that their molecules were also located along the minor groove of DNA.

In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg 2+ or Na + ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg 2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na + ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA.

The interaction of the regulatory biologically active peptide Glu-Asp-Arg (EDR) with DNA is considered by spectral, NMR, viscosimetry, and molecular dynamics methods. It was shown that EDR can partly penetrate into the major groove of DNA and affect the base atoms, mainly the N7 and O6 of guanine. It was observed that Mg 2+ ions can promote DNA−EDR interaction due to their effective screening of the negatively charged phosphate groups of DNA. This action of Mg 2+ remains in salted solution as well.

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