Supramolecular complex formed by DNA oligonucleotide and thiacalix[4]arene. NMR-spectroscopy and molecular docking

• Complexation of calixarene with DNA was studied using NMR and molecular docking.
• From docking simulations we select the complexes compatible with NMR constraints.
• Oligonucleotide in solution exists in double- and single-stranded helixes.

The combination of NMR-spectroscopy and molecular docking was applied to investigate the complexation of thiacalix[4]arene with DNA. We have studied the structure of supramolecular complex formed by palindromic decamer DNA d(GCGTTAACGC)2 and tetrasubstituted at lower rim of p-tert-butyl thiacalix[4]arene in 1,3-alternate conformation. With the help of NMR it is shown that oligonucleotide in solution exists in two states: double-stranded helix (dominant structure in solution) and single-stranded form (minor structure) rolled up in a “hairpin” with equilibrium between them. Both complementary methods, NMR and molecular docking, revealed the formation of molecular complex by thiacalix[4]arene and palindromic decamer DNA. Different possible conformations of the complexes were analyzed by means of molecular docking. We used the experimental constraints in molecular docking to identify the complexes, which were in agreement with the NMR data.

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