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Publication Abstract from PubMed

A parallel quadruplex derived from the Myc promoter sequence was extended by a stem-loop duplex at either its 5'- or 3'-terminus to mimic a quadruplex-duplex (Q-D) junction as a potential genomic target. High-resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl sidechain was shown to bind the Q-D hybrids with a very high affinity in the order K a ~ 10 7 M -1 irrespective of the duplex location at the quadruplex 3'- or 5'-end. NMR chemical shift perturbations identified the tetrad face of the Q-D junction as specific binding site for the ligand. However, calorimetric analyses revealed significant differences in the thermodynamic profiles upon binding to hybrids with either a duplex extension at the quadruplex 3'- or 5'-terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3'-Q-D junction, whereas non-hydrophobic entropic contributions favor binding with formation of a 2:1 ligand-quadruplex complex in case of the 5'-Q-D hybrid.

Quadruplex-Duplex Junction: A High-Affinity Binding Site for Indoloquinoline Ligands.,Vianney YM, Preckwinkel P, Mohr S, Weisz K Chemistry. 2020 Sep 25. doi: 10.1002/chem.202003540. PMID:32975874^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.