title: Spectroscopic and calorimetric studies on the binding of an indoloquinoline drug to parallel and antiparallel DNA triplexes.
abstract: 11-Phenyl-substituted indoloquinolines have been found to exhibit significant antiproliferative potency in cancer cells but to show only moderate affinity toward genomic double-helical DNA. In this study, parallel as well as antiparallel triple-helical DNA targets are employed to evaluate the triplex binding of these ligands. UV melting experiments with parallel triplexes indicate considerable interactions with the drug and a strong preference for TAT-rich triplexes in line with an increasing number of potential intercalation sites of similar binding strength between two TAT base triads. Via substitution of a singly charged aminoethylamine side chain by a longer and doubly charged bis(aminopropyl)amine substituent at the ligand, binding affinities increase and also start to exhibit long-range effects as indicated by a strong correlation between the binding affinity and the overall length of the TAT tract within the triplex stem. Compared to parallel triplexes, an antiparallel triplex with a GT-containing third strand constitutes a preferred target for the indoloquinoline drug. On the basis of pH-dependent titration experiments and corroborated by a Job analysis of continuous variation, binding of the drug to the GT triplex not only is strongly enhanced when the solution pH is lowered from 7 to 5 but also reveals a pH-dependent stoichiometry upon formation of the complex. Calorimetric data demonstrate that stronger binding of a protonated drug at acidic pH is associated with a more exothermic binding process. However, at pH 7 and 5, binding is enthalpically driven with additional favorable entropic contributions.
authors.affiliation: Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany.
authors.forename: Fanny
authors.initials: F
authors.lastname: Riechert-Krause
authors.forename: Karolin
authors.initials: K
authors.lastname: Autenrieth
authors.forename: Andrea
authors.initials: A
authors.lastname: Eick
authors.forename: Klaus
authors.initials: K
authors.lastname: Weisz
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D007364:Intercalating Agents / Q000737:chemistry* / Q000494:pharmacology*; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011804:Quinolines / Q000737:chemistry* / Q000494:pharmacology*; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D007364:Intercalating Agents; D011804:Quinolines; C051802:triplex DNA; D004247:DNA