All-atoms classical Molecular Dynamics of Nucleosome containing 8oxoGuanine:C and 8oxoGuanine:A

Amber topology files and nc/dcd trajectory files of nucleosome core particule based on the cryoEM structures with 0.10 M of NaCl salt. Four positions of 8oxoGuanine:C (C1 to C4 system) and 8oxoGuanine:A (A1 to A4) lesions are considered (). Control data are included, for undamaged nucleosome sequence (CONTROL) and free oligonucleotide damaged and undamaged sequence (Oligo). Each trajectory is of 1 µs. Force field used: Amber14ff + parmbsc1, TIP3P water model, Hydrogen Mass Repartitioning, CUFIX correction. The water molecules and ions were stripped. prod.in: input file for production trajectory. Position from the Dyad: 1 = +64 (8oxoG on complementary strand) SHL -6 2 = -37 SHL +4 3 = -27 SHL +3 4 = -19 SHL +2