Thermodynamics and kinetics of Lesion Induced DNA Amplification (LIDA)

Non-enzymatic short-chain XNA replication is often prohibited due to product inhibition, and product inhibition has been one of the major stumbling blocks for implementing prebiotic information replication systems both in bulk 4 and as part of synthetic protocells. 7 Product inhibition implies that a newly formed complementary template is very unlikely to dehybridize from the template. However, Gibbs-Davis and her team 1 have developed a method to circumvent product inhibition based on mismatches and lesions between the complementary templates that destabilize them and thus enables a continued replication process. In this work we explore in simulation the thermodynamic and kinetic properties of lesion induced DNA amplification processes. The method we use focuses on a characterization of the oligomers by their free energies rather than by their detailed base-pair structure.