The Thermodynamic and Kinetic Properties of the dA-rU DNA-RNA Hybrid Base Pair Investigated via Molecular Dynamics Simulations

Abstract

DNA-RNA hybrid duplexes play essential roles during the reverse transcription of RNA viruses and DNA replication. The opening and conformation changes of individual base pairs are critical to their biological functions. However, the microscopic mechanisms governing base pair closing and opening at the atomic level remain poorly understood. In this study, we investigated the thermodynamic and kinetic parameters of the dA-rU base pair in a DNA-RNA hybrid duplex using 4 μs all-atom molecular dynamics (MD) simulations at different temperatures. Our results showed that the thermodynamic parameters of the dA-rU base pair aligned with the predictions of the nearest-neighbor model and were close to those of the AU base pair in RNA. The temperature dependence of the average lifetimes of both the open and the closed states, as well as the transition path times, were obtained. The free-energy barrier for a single base pair opening and closing arises from an increase in enthalpy due to the disruption of the base-stacking interactions and hydrogen bonding, along with an entropy loss attributed to the accompanying restrictions, such as torsional angle constraints and solvent viscosity.

Keywords: DNA-RNA hybrid; base pair; kinetics; molecular dynamics simulation; thermodynamics.

Figure 1

The two typical structures of a DNA-RNA hybrid with closed and open terminal base pairs: (left), closed state; (right), open state.

Figure 2

(a) The RMSD values and torsional angles ζ for the dA-rU base pair over the entire simulation period at 370 K. (b) The distribution of the RMSD of the dA-rU base pair over the entire simulation period at 370 K. (c) The distribution of the torsional angles ζ of the dA-rU base pair over the entire simulation period at 370 K.

Figure 3

(a) The RMSD values and (b) torsional angles ζ for the simulation period from 262 to 284 ns at 370 K. (c) The RMSD values and torsional angles ζ near the transition states at 370 K.

Figure 4

(a) The probability in the closed state over the simulation time for each temperature. (b) The temperature dependence of ln(p_op/p_cl) at 370 K, 380 K, 390 K, and 400 K. Line: line fit; square: simulation results.

Figure 5

(a) Temperature dependence of the average lifetime of the closed state (square) and the open state (circle). Lines: fitted with Equation (3); symbols: MD simulations. (b) Temperature dependence of the ratios of $t_{cl}/t_{tp}^{\mathrm{c}\to \mathrm{o}}$(circle) and $t_{op}/t_{tp}^{\mathrm{o}\to \mathrm{c}}$ (square). Lines: fitted with Equations (3) and (4); symbols: MD simulations.