The conference “Chemical Biology: Fundamental Problems of Bionanotechnology” devoted to the 25 anniversary of the Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences took place in Novosibirsk on 10–14 of June 2009. Organizers were the Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Acad emy of Sciences (ICBFM SB RAS) and the Siberian Branch of the Russian Academy of Sciences. The conference was opened with the plenary lec ture of academician A.I. Archakov “International project ‘Human proteome’: present and future aspects.” Urgent problems of bionanotechnology were discussed in lectures of the sections: Bionansensors and diagnostics of nanostructures (the basis of biosen sors, physical methods of analysis of bionanomateri als); Bionanodevices, bionanomachines, and bio nanocatalysis; Principles in the self organization of bionanostructures and synthesis of hybrid bionano composites; and Nanoobjects in biotechnology and medicine (nanotransfectants, nanosafety, nanostruc tural materials). The lecture of O.I. Lavrik (ICBFM SB RAS) was dedicated to organization of the protein nanoma chines, which provide effective DNA reparation essential for cell resistance to oxidative stress, chemo therapeutics, and ionizing irradiation. Mechanisms of base reparation and single and double strained DNA brakes are provided by specific protein ensembles that form temporary complexes for recovery of disrupted DNA regions. During a process of intermediate com plexes organization, the important role is played by cofactors of reparation that execute a function of coordinators of the consequent stages of DNA repara tion. The lecture contained material about cofactor proteins of the base reparation process: Poly (ADP ribose) polymerase 1 and XRCC1. The role of these proteins in coordination of DNA polymerase beta, apurinic/apyrimidinic endonuclease 1, and flap endonuclease 1 functions was reviewed. When pro teins and nucleic acids as nanoobjects interact with the low molecular ligands or other biopolymers, there are some conformational changes in the studied struc tures. For study of conformational transitions in pro teins and nucleic acids, the most informative method is the method of “stopped stream” in combination with the appropriate registration approach. As a highly sensitive component in the registration system, speak ers V.V. Koval and O.S. Fedorova (ICBFM SB RAS) suggested to use tryptophan residues. It is the inten sively fluorescent amino acid allowing using it as the marker of conformational changes in protein mole cules that is necessary for evaluation of kinetic and thermodynamic characteristics of biopolymer interac tion with the specific ligands and substrates in nano carriers. In the construction of biological nanosys tems, one of the main problems is the mechanism of nanoobject delivery to the target point. In the lecture of D.O. Zharkov (ICBFM SB RAS) was reviewed a topic of creation of delivery ways called “nanorails.” In the life systems and the eukaryotic cells, the function of transport of certain intracellular elements is maintained by the cytoskeleton. A lot of proteins and protein complexes that play their roles in genetic information realization are shifting along the DNA or RNA strains “searching” for specific ele ments of recognition (restriction sites, promoters, etc.) Use of DNA as the nanorails may be estimated as preferred. One of the shifting mechanisms is the non targeted one dimensional diffusion without energy consumption. The author had developed a new approach to the quantitative analysis of such mecha nism. It was shown that the number of DNA repara tion enzymes (DNA glycosilases, AP endonucleases) are shifting due to one dimensional diffusion. Mutant forms of these proteins with changed abilities of DNA railed moving are derived. They may find their appli cation in biotechnology for targeted delivery of nano systems. Among medical bionanotechnology problems, the main attention of represented lectures was dedicated to the approaches of drug targeted delivery to the place of their function in the organism. Multipurpose nano compositions based on self assembling effect of inor ganic organic polymer structures were applied by B.G. Sukhov and B.A. Trofimov (A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Rus sian Academy of Sciences). The idea of the process is encapsulation of nanoparticles of different nature including metal oxides in the volumetric biopolymer “screen” (arabinogalactan, galactomannan, heparin, humic acids etc.).