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High\u2010resolution structures of the hybrids demonstrate continuous stacking of the duplex on the quadruplex core without significant perturbations. An indoloquinoline ligand carrying an aminoalkyl side chain was shown to bind the Q\u2013D hybrids with a very high affinity in the order <jats:italic>K<\/jats:italic><jats:sub>a<\/jats:sub>\u224810<jats:sup>7<\/jats:sup>\u2005<jats:sc>m<\/jats:sc><jats:sup>\u22121<\/jats:sup> irrespective of the duplex location at the quadruplex 3\u2032\u2010 or 5\u2032\u2010end. NMR chemical shift perturbations identified the tetrad face of the Q\u2013D 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\u2032\u2010 or 5\u2032\u2010terminus. A large enthalpic gain and considerable hydrophobic effects are accompanied by the binding of one ligand to the 3\u2032\u2010Q\u2013D junction, whereas non\u2010hydrophobic entropic contributions favor binding with formation of a 2:1 ligand\u2010quadruplex complex in case of the 5\u2032\u2010Q\u2013D hybrid.<\/jats:p>","DOI":"10.1002\/chem.202003540","type":"journal-article","created":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T11:08:23Z","timestamp":1601032103000},"page":"16910-16922","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Quadruplex\u2013Duplex Junction: A High\u2010Affinity Binding Site for Indoloquinoline Ligands"],"prefix":"10.1002","volume":"26","author":[{"given":"Yoanes Maria","family":"Vianney","sequence":"first","affiliation":[{"name":"Institute of Biochemistry Universit\u00e4t Greifswald  Felix-Hausdorff-Str. 4 17487 Greifswald 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