MD simulations were performed for the G4-duplex DNA constructs containing the wild-type and mutant chair (PDB ID: 2KM3 and see Supplementary Data for details), 2-tetrad basket (PDB ID: 2KF8), hybrid 1 (PDB ID: 2JSM) and hybrid 2 G4 conformations (PDB ID: 2JSL). All MD simulations were performed with generalized born implicit solvent (GBIS) in NAMD (36) version 2.9 with bonds to hydrogen atoms held rigid using an integration step of 2 fs. The simulation temperature of 298 K was maintained by the Langevin piston method with a damping coefficient of 1 ps−1. For the non-bonded interactions a switching function was used with a switching distance of 15 Å and with an 18 Å cutoff. The AMBER parm99bsc0 force field parameters with χOL4 corrections (37,38) in CHARMM format have been applied to DNA in all simulations. The DNA terminals were terminated according to standard AMBER topology. The solvent was described by the GBIS algorithm with a dielectric constant of 78.5 and implicit ions were included to a concentration of 0.15 M. In total 1.5–2.0 μs simulation was produced for each of G4 conformations. Sufficient sampling was achieved for all constructs (Supplementary Figure S4). Further details on MD simulations are provided in the Supplementary Data.