Theoretical and experimental investigations of DNA open states

Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in DNA, for example. A comparative analysis of experimental data on the kinetics and thermodynamics of DNA open states for a wide temperature range was carried out. Discrepancies between the results of various experiments have been explained. Three types of DNA open states are recognized based on their differences in thermodynamic properties and other characteristics. Besides, an upto-date definition of the term “open state” is given. A review is carried out for simple mathematical models of DNA in most of which the state of one pair is described by one or two variables. The main problems arising in theoretical investigations of heterogeneous DNA in the framework of models of this level are considered. The role of each group of models in interpretation of experimental data is discussed. Special сonsideration is given to the studies of the transfer and localization of the nucleotide pairs oscillations’ energy by mechanical models. These processes are shown to play a key role in the dynamics of a heterogeneous duplex. Their theoretical interpretation is proven to be very important for the development of modern molecular biology and biophysics. The main features of the theoretical approaches are considered which enabled describing various experimental data. Prospects of the models’ development are described, particular details of their optimization are suggested, and possible ways of modernization of some experimental techniques are discussed.