Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site

DNA duplex stability arises from cooperative interactions between multiple adjacent nucleotides that favor base pairing and stacking when formed as a continuous stretch rather than individually. Lesions and nucleobase modifications alter this stability in complex manners that remain challenging to understand despite their centrality to biology. Here, we investigate how an abasic site destabilizes small DNA duplexes and reshapes base pairing dynamics and hybridization pathways using temperature-jump infrared spectroscopy and coarse-grained molecular dynamics simulations. We show how an abasic site splits the cooperativity in a short duplex into two segments, which destabilizes small duplexes as a whole and enables metastable half-dissociated configurations. Dynamically, it introduces an additional barrier to hybridization by constraining the hybridization mechanism to a step-wise process of nucleating and zipping a stretch on one side of the abasic site and then the other.

Python scripts for generating abasic configurations from intact 3SPN.2 files, performing metadynamics simulations, and reweighting free energy surfaces are available at https://github.com/mrjoness/abasic-thermo/ (68). Scripts for running equilibrium simulations and building Markov State models are available at https://github.com/mrjoness/abasic-kinetics/ (69). All PLUMED input scripts were submitted to the PLUMED-NEST public repository and are available at https://www.plumed-nest.org/eggs/22/037/ (70). All unbiased and biased MD trajectories (65 GB), time- and rate-domain t-HDVE data, FTIR temperature series, and experimental and 3SPN.2-determined melting curves are uploaded to Zenodo and available at https://doi.org/10.5281/zenodo.7199303 (71).