Project files provided as supporting information to the manuscript "Sequence- and supercoiling-dependent effects on the structural dynamics of DNA minicircles"

README file to the project files provided as supporting information to the manuscript. Authors: Manuel Micheloni, Luca Tubiana, Raffaello Potestio, Lorenzo Petrolli ================================== The main directory contains this readme file and two compressed archives: EqDNAMini.tar.gz and SynthBubble.tar.gz. EqDNAMini.tar.gz includes MD simulations of a 672-bp DNA minicircle at six values superhelical densities. Each simulation scenario is stored in a separate subfolder named according to its superhelical density (i.e., Sigma_-0.1, Sigma_-0.08, Sigma_-0.06, Sigma_0, Sigma_0.06, and Sigma_0.1). SynthBubble.tar.gz contains simulations of the DNA minicircle at a fixed superhelical density of –0.06, with synthetic DNA bubbles of different sizes enforced in the same supercoiled region. These simulations are organized in subfolders as B1, B2, B5, and B10, corresponding to bubble sizes of 1, 2, 5, and 10 bp, respectively. Each subfolder (e.g., Sigma_* and B*) contains a data, input_structure and MD_scripts directory. The data directory includes three subfolders: 1.E: for each independent MD replica, the folder contains the internal energy data files of the DNA minicircle (both for the relaxation and the production run stage) and the pairwise energy contribution between complementary nucleotides in the DNA helix (production run only); 2.traj: it contains the MD trajectories of the DNA minicircle for each replica (both the relaxation and production run stage). The /MD_scripts folder contains the scripts used to perform the molecular dynamics simulations. The /input_structure folder contains the configuration and topology (in the oxDNA format) files used for each MD run. The DNA template used in all MD simulations is based on the work of Fogg and colleagues [1]. NOTE: Data files related to the relaxation stage of each simulation contain “Relax1” in their filenames, while files associated with the production run stage are labeled with “Relax2. For details about the simulation protocol employed in either stage, please refer to the main text of the work. [1] Fogg, J.M., Judge, A.K., Stricker, E. et al. Supercoiling and looping promote DNA base accessibility and coordination among distant sites. Nat Commun 12, 5683 (2021). https://doi.org/10.1038/s41467-021-25936-2