Expanding the DNA Damaging Potential of Artificial Metallo-Nucleases with Click Chemistry

This dataset contains all structure, topology, parameter, and trajectory files associated with the molecular dynamics (MD) simulations of the Cu₃-TC-Py complex bound to the Dickerson–Drew dodecamer (DDD) DNA duplex. The simulations were performed to explore the stability and binding energetics of Cu₃-TC-Py within the major and minor grooves of B-form DNA.

All-atom MD simulations were carried out using the CHARMM36 force field with explicit TIP3P water and neutralizing counterions under periodic boundary conditions. The initial coordinates were derived from the highest-affinity major and minor groove docking poses, followed by 4 µs of production dynamics for each system in the NPT ensemble.

The files in this repository include:

• XYZ coordinates of starting complexes (major and minor groove bound)

• Topology and parameter files for DNA, Cu₃-TC-Py, and solvent/ions

• Input files for GROMACS (energy minimization, equilibration, and production)

• Trajectory files (coordinate and log outputs)

• Force field parameter references compatible with CHARMM36

These simulations demonstrate that the Cu₃-TC-Py complex remains bound within both grooves throughout the trajectories, confirming its high DNA affinity. Analysis of Coulombic and van der Waals interaction energies showed that electrostatic interactions dominate binding, with enhanced stability observed for the minor groove configuration.

All data are provided to ensure full reproducibility of the MD simulations described in the manuscript.