The Thermodynamics And Kinetics Of A Nucleotide Base Pair

RNA is a key biological macromolecule that functions in various cellular processes, such as transcription, translation and the conservation of genetic information. However, RNA adopts a variety of complex secondary or three-dimensional structures, a characteristic central to its role in diverse biological functions. In the process of structural rearrangement, the closing and opening of base pairs are fundamental events, and the formation of biologically relevant structures is often kinetically controlled and dependent on the relative kinetic rates of base pair opening and closing. Therefore, understanding the thermodynamic and kinetic properties of the closing and opening of a single base pair is vital for a quantitative understanding of the biological functions of many RNA molecules.Because the unfolding of RNA double helices at room temperature is quite slow, we simulated the base pair opening-closing switch near its melting temperature, which can quickly lead to the equilibration of base pair opening and closing. The thermodynamic parameters and the kinetic mechanism of single base pair were obtained through molecular dynamics simulations at high temperatures. Furthermore, the impact of ions concentration and the nearest neighbor base pair on the thermodynamics and kinetics of single base pair were also obtained. The main research contents are as follows:(1) The thermodynamics and kinetics of a nucleotide base pairWe proposed a method to characterize the closed states, open states and transition state of single base pair from the dynamic simulation trajectory. The thermodynamic parameters and the opening-closing switching characteristic of single base pair were obtained according to the simulation trajectory at different temperature 390K,400K,410K,420K and 430K. In thermodynamic, the enthalpy change AH and the entropy change ?S of the base pair were obtained through the equilibrium population distribution of the open and closed states at different temperatures. The computed results were consistent with the thermodynamic parameters of the nearest-neighbor model. In kinetics, the average lifetime of the closed state, open state and transition state were obtained. Furthermore, the opening rate, closing rate and transition path rate were also obtained, and the closing and opening rates showed different temperature dependences. The transition path time also exhibited weak temperature dependence and was insensitive to the energy barrier.These results suggest that breaking a single base pair mainly involves the enthalpy increase, AH, due to the disruption of hydrogen bonding and the base-stacking interactions. Formation of a single base stack, however, mainly involves the unfavorable entropy loss, AS, due to the accompanying restriction from the torsional angles, the viscosity of the solvent and so on. Therefore, this further illustrate that one-dimensional free energy surface was sufficient to accurately describe the dynamics of the base pair opening and closing, and the dynamics were Brownian, and the diffusion constant showed super-Arrhenius behavior.(2) The impact of ions concentration on the thermodynamics and kinetics of single base pairThe thermodynamic parameters and the opening-closing switching characteristic of single base pair were obtained at different ions concentration, which is 0.5M,0.1M and 0.05M, and the impace of ions concentration was also researched. In thermodynamic, the enthalpy change AH and the entropy change AS of the base pair were obtained at different ions concentration. It was found that the enthalpy is not effected by the ions concentration, however, the entropy is effected and decreases with decreased ions concentration, which is consistent with experimental results. In kinetics, according to the average lifetime of open state, closed state and transition state, it was found that the average lifetime of closed state and transition state were not vary with the different ions concentration, however, the average lifetime of open state increase with decreasing ions concentration, which is also consistent with experimental results.These results suggest that breaking a single base pair under different ions concentration mainly involves the same enthalpy increase, therefore, the opening rates do not change with the different ions concentration. However, in the process of formation of a single base stack, as the potential energy surface roughness varies with the different ions concentration. When the ions concentration is smaller, the potential energy surface is more rough, and the trap states is much more, so the closing rates is slower, which is consistent with experimental results.(3) The impact of the nearest neighbor base on the thermodynamics and kinetics of single base pairThe thermodynamics parameters and the opening-closing switching characteristic of base pair GC (3'-CC… 5'-GG…)?GG((3'-CC… 5'-GG…) at the different nearest neighbor base were obtained at the ions concentration 0.5M. These results suggested that the thermodynamics parameters, the enthalpy change AH and the entropy change AS, were impacted by the nearest neighbor base pair, and in kinetics, there have a great influence on the average lifetime and transition rates. In addition, the potential energy surface roughness is also different as the different nearest neighbor base pair, which is consistent with experimental results.