Thermodynamics of DNA Hybridization from Atomistic Simulations

Studying DNA hybridization equilibrium at atomistic length scales, either via molecular dynamics (MD) or through commonly used advanced sampling approaches, is notoriously difficult. In this work, we describe an order-parameter-based technique to calculate the free energy of hybridization, and estimate melting temperature oligomers resolution. The landscapes are reported as a function native-topology-based order parameter for Drew–Dickerson dodecamer range decamer sequences different GC content. Our estimated temperatures match experimental numbers within ±15 °C. As test numerical reliability procedures employed, it was verified that predicted surfaces d- l-enantiomers were indistinguishable accuracy.