Coordinates for initial structures were taken from the X-ray structures: d(G4T4G4)2 G-DNA (PDB: 2GWQ, resolution 2.00 Å, the first molecule in the crystal lattice); d(TGGGT)4 G-DNA (PDB: 352D, resolution 0.95 Å)27 (link); r(UGGGGU)4 G-RNA (PDB: 1J8G, resolution 0.61 Å)28 (link) and (CGCGCG)2 Z-DNA (PDB: 1I0T, resolution 0.6 Å)29 (link).
All simulations of d(G4T4G4)2 started with three ions in the channel and two additional ions at the stem loop junctions, as seen in the X-ray structure. The stem-loop junction ions were, however, quickly lost, as discussed elsewhere.22 d(TGGGT)4 structure contains unpaired thymidine residues at the ends of all strands, involved in crystal packing interactions. We removed these residues from the simulated structures to prevent structure fluctuations caused by fluctuations of these unpaired residues. The structure of r(UGGGGU)4 was obtained as the biological assembly deposited in the database. We again removed the flanking uridines. Strontium cations in the channel were replaced by either sodium or potassium cations. For both parallel quadruplexes, we modified numbering of the nucleotides according to theFigure 1 . Structure of Z-DNA hexamer was manually lengthened to dodecamer by repeating and translating the helix to allow stable simulations. Spermine molecule was not included in the simulations.
The structures were prepared using the tLeap module of AMBER 10.30 Systems were neutralized by adding monovalent counterions, either K+ or Na+ (with different parameter sets as described later). Besides simulations with net-neutralization, KCl excess salt simulations were also conducted. Added ions were distributed around the molecule by tLeap according to the solute electrostatic potential. Molecules were placed into truncated octahedral box of explicit water solvent with minimal distance of 10 Å of solute from the box border.
All simulations of d(G4T4G4)2 started with three ions in the channel and two additional ions at the stem loop junctions, as seen in the X-ray structure. The stem-loop junction ions were, however, quickly lost, as discussed elsewhere.22 d(TGGGT)4 structure contains unpaired thymidine residues at the ends of all strands, involved in crystal packing interactions. We removed these residues from the simulated structures to prevent structure fluctuations caused by fluctuations of these unpaired residues. The structure of r(UGGGGU)4 was obtained as the biological assembly deposited in the database. We again removed the flanking uridines. Strontium cations in the channel were replaced by either sodium or potassium cations. For both parallel quadruplexes, we modified numbering of the nucleotides according to the
The structures were prepared using the tLeap module of AMBER 10.30 Systems were neutralized by adding monovalent counterions, either K+ or Na+ (with different parameter sets as described later). Besides simulations with net-neutralization, KCl excess salt simulations were also conducted. Added ions were distributed around the molecule by tLeap according to the solute electrostatic potential. Molecules were placed into truncated octahedral box of explicit water solvent with minimal distance of 10 Å of solute from the box border.