Theoretical and Experimental Investigations of DNA Open States
Shigaev A.S., Ponomarev O.A., Lakhno V.D.
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, 142290, Pushchino, Moscow Region, Russia
Abstract. This research is a review and assay of literature data on the properties of DNA open states. The states result from large fluctuations of a duplex and have a great influence on a wide range of biochemical processes, including electric charge transfer in DNA. A comparative analysis of kinetic and thermodynamic experimental data on DNA open states has been performed for a wide temperature range. Apparent contradictions between the data of different experiments have been explained. Based on differences in thermodynamic properties and other characteristics three different types of DNA open states have been identified; a modern definition of the term "open state" has been given. A brief review of simple mathematical models of DNA has been presented; in most of the models the state of every base pair is defined by one or two variables. The central problems of investigation of heterogeneous DNA within the approaches of the level considered are examined. The roles of every model group in experimental data interpretation are discussed. Special emphasis is placed on the study of transfer and localization of base pair vibration energy in mechanical models. These processes have been shown to play a key role in heterogeneous duplex dynamics, and their theoretical treatment is critically important for the development of modern molecular biology and biophysics. The key features of theoretical approaches, that enabled description of various experimental data, have been considered. The future development of the models has been desribed, some particular details of their optimization have been suggested; probable ways of improving some experimental techniques have been proposed.
Key words: DNA models, DNA dynamics, energy transfer, energy localization, DNA open state, denaturation bubble, base pair flip-out.