S.S. Antipov, V.O. Pokusaeva, V.V. Melekhov, O.N. Ozoline

Dps protein (DNA-binding Protein of Starved cells) of E.coli is one of the nucleoid-associated proteins whose expression significantly increases in the stationary phase of growth. Dps dodecamer is a multifunctional protein. It protects bacterial DNA from various types of damage by oxidizing Fe2 + to Fe3 + and depositing of 400-500 iron oxide molecules inside the protein cavity. There are no conventional DNA-binding modules in the 3D-structure of Dps, so the way of its interaction with DNA is yet unknown. Multifunctional properties of Dps protein, precisely the ability to bind DNA tightly and form within the protein cavity mineralized core with intrinsic magnetic moment, dependence on microwave irradiation, imply the controllable immobilization of Dps on DNA - forming matrix. It could enable the creation of predetermined distribution of fixed composition and size ferromagnetic particles. Therefore, a thorough analysis of DNA-Dps interaction is extremely relevant. The efficiency of nucleoprotein complex formation with the protein Dps was investigated as a function of the electrostatic potential, the magnitude of the anisotropic bending and thermodynamic stability of the model DNA fragments taken from the genome of E.coli. For comparison, we used four fragments, two of which were derived from the promoter regions of genes dps and hns, one of the hns coding sequence and one represented transcriptionally inactive «promoter island» located within the gene yeaI. All fragments formed complexes with Dps, which is consistent with the general point of view that Dps is capable to bind any nucleotide sequences. But efficiency of interaction appeared to be different, which is the first indication, assuming certain binding specificity. DNA fragment containing the A/T-rich sequence of the gene yeaI interacted with Dps most effectively. That means that the thermodynamically unstable and therefore easily deformable nucleotide sequences may be the preferred targets for Dps, which is the major protein of bacterial nucleoid, condensing bacterial genome and protecting it from different damages during stationary growth and under different stresses.