Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations

In this work, we present a kinetic Markov state Monte Carlo model designed to complement temperature-jump (T-jump) infrared spectroscopy experiments probing the kinetics and dynamics of short DNA oligonucleotides. The is be accessible experimental researchers in terms both computational simplicity expense while providing detailed insights beyond those provided by methods. an extension thermodynamic lattice for hybridization utilizing formalism nucleation-zipper mechanism. Association dissociation trajectories were generated Gillespie algorithm parameters determined via fitting association timescales previously published data. Terminal end fraying, experimentally observed following rapid T-jump, sequence 5′-ATATGCATAT-3′ was replicated that also demonstrated fast sequences 5′-C(AT)nG-3′, where n = 2–6, due terminal fraying. dominant pathways, isolated transition pathway theory, showed two primary motifs: initiating at or next G:C base pair, which enthalpically favorable related increased strength pairs, center sequence, entropically minimizing penalty associated with decrease configurational entropy hybridization.