The DNA molecule is the biological polymer related to some of the most important vital processes, from the storage and transmission of genetic information to the translation of proteins. In vivo, many of the intracellular processes are mediated by interactions between the DNA molecule and ligands like proteins and enzymes. On the other hand, DNA interactions with drugs are important in the treatment of many human diseases, especially in cancer chemotherapies. In fact, some classes of drugs such as the anthracyclines and the platinum-based compounds exhibit a strong affinity to interact with the DNA of cancer cells. When these drugs bind to DNA they can inhibit the replication process, thus stopping tumor growth.
DNA interactions with ligands such as drugs and proteins is a multidisciplinary field in which physicists, biologists and chemists share knowledge on the biophysics and biochemistry of such interactions, which can be investigated both theoretically and experimentally. From the theoretical point of view, analytical modeling and simulations are usually used to investigate many aspects of the DNA-ligand complexes such as the association energies and binding site sizes. Experimentally, there are basically three different types of techniques usually used to investigate these systems: single molecule stretching, single molecule imaging and ensemble-averaging techniques. In single molecule stretching such as optical or magnetic tweezers, the DNA-ligand complexes can be manipulated and stretched individually, and their mechanical properties can be deduced from force-extension measurements. Since these mechanical properties are usually changed when the ligands bind to the DNA double-helix, the physical chemistry of the interaction can be deduced from such measurements. In fact, in the past years many advances were achieved in order to connect the mechanics to the physical chemistry of these systems, such that one can deduce physicochemical properties from pure mechanical ones, or vice-versa. In single molecule imaging, performed for example by atomic force microscopy, the mechanical parameters can be deduced directly from the conformation of individual molecules, and the physical chemistry can then be studied as well. In addition, the recent advances in super-resolution fluorescence microscopy are giving insights on important information such as protein binding sites and the dynamic action of enzymes on the DNA structure. Finally, from ensemble-averaging techniques such as dynamic light scattering, optical spectroscopies and gel electrophoresis, the interactions can be monitored by analyzing the collective behavior of a set of many molecules.
This special issue will publish new theoretical and experimental studies on biophysics and biochemistry of the DNA interactions with drugs, proteins, enzymes and other types of ligands. The topics of primary interest include, but are not limited to: “DNA interactions characterization by single molecule and ensemble-averaging techniques”, “Mechanics and physical chemistry of DNA-ligand complexes”, “DNA polyelectrolyte solutions”, “DNA condensation”, “Cancer at molecular level” and “DNA-ligand interactions simulation”.