Calculation of Energy for RNA/RNA and DNA/RNA Duplex Formation by Molecular Dynamics Simulation

Abstract The development of approaches for predictive calculation hybridization properties various nucleic acid (NA) derivatives is the basis rational design NA-based constructs. Modern advances in computer modeling methods provide feasibility these calculations. We have analyzed possibility calculating energy DNA/RNA and RNA/RNA duplex formation using representative sets complexes (65 75 complexes, respectively). used classical molecular dynamics (MD) method, MMPBSA or MMGBSA to calculate enthalpy (? H °) component, quasi-harmonic approximation (Q-Harm) normal mode analysis (NMA) entropy S contribution Gibbs ( $$\Delta G_{{37}}^{^\circ }$$ ) NA complex formation. found that method MD trajectory only empirical linear allow DNA, RNA, hybrid duplexes lengths GC content with an accuracy 8.6%. Within each type complex, combination rather efficient Q-Harm being applied bimolecular makes it possible error value 10%. high different types natural (DNA/RNA, DNA/RNA, RNA/RNA) indicates extending considered approach analogs acids, which gives a fundamental opportunity future perform new NA-targeted sequence-specific compounds.