Computational protocol: Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity†

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Protocol publication

[…] Inter-proton distances for J19 () were classified based on NOESY experiments performed in H2O (mixing time, 200 ms) and D2O (mixing times, 100, 200 and 300 ms), and were duplicated for the two monomers. In vacuum, models were generated using the XPLOR-NIH program () in two general steps: (i) distance geometry simulated annealing and (ii) distance-restrained molecular dynamics refinement. Hydrogen-bond restraints, inter-proton distance restraints, dihedral restraints, planarity restraints, and non-crystallographic symmetry restraints were imposed during structure calculations. Ten lowest-energy structures were then subjected to distance-restrained molecular dynamics refinement in explicit solvent using the AMBER program (), in which the dihedral, planarity and noncrystallographic symmetry restraints were removed. Detailed procedures are described in the Supplementary Data. Structures were displayed using the PyMOL program (). […]

Pipeline specifications

Software tools Xplor-NIH, AMBER, PyMOL
Application NMR-based proteomics analysis