Porphyrin binding mechanism is altered by protonation at the loops in G-quadruplex DNA formed near the transcriptional activation site of the human c-kit gene

• Published in: Biochimica et biophysica acta Vol. 1820; no. 12; pp. 1987 - 1996
• Main Authors: Manaye, Sintayehu, Eritja, Ramon, Aviñó, Anna, Jaumot, Joaquim, Gargallo, Raimundo
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.12.2012
• Subjects: absorption; adenine; antineoplastic agents; c-kit; Conformational analysis; cytosine; denaturation; DNA; Expressió gènica; G-quadruplex; G-Quadruplexes; Gene expression; homeostasis; Humans; Hydrogen-Ion Concentration; Kinetics; Ligand; Multivariate analysis; Oncogenes; Oncogens; Porfirines; Porphyrins; Porphyrins - metabolism; Proto-Oncogene Proteins c-kit - chemistry; Proto-Oncogene Proteins c-kit - genetics; Proto-Oncogene Proteins c-kit - metabolism; proto-oncogenes; Stacking interactions; Substrate Specificity; Surface Plasmon Resonance; Telomere; telomeres; Telòmer; titration; Transcription, Genetic; Transcriptional Activation; Stacking interactions; Multivariate analysis; c-kit; Ligand; G-quadruplex; Conformational analysis
• ISSN: 0304-4165; 0006-3002; 1872-8006
• DOI: 10.1016/j.bbagen.2012.09.006

G-quadruplex DNA structures are hypothesized to be involved in the regulation of gene expression and telomere homeostasis. The development of small molecules that modulate the stability of G-quadruplex structures has a potential therapeutic interest in cancer treatment and prevention of aging. Molecular absorption and circular dichroism spectra were used to monitor thermal denaturation, acid base titration and mole ratio experiments. The resulting data were analyzed by multivariate data analysis methods. Surface plasmon resonance was also used to probe the kinetics and affinity of the DNA–drug interactions. We investigated the interaction between a G-quadruplex-forming sequence in the human c-kit proto-oncogene and the water soluble porphyrin TMPyP4. The role of cytosine and adenine residues at the loops of G-quadruplex was studied by substitution of these residues by thymidines. Here, we show the existence of two binding modes between TMPyP4 and the considered G-quadruplex. The stronger binding mode (formation constant around 107) involves end-stacking, while the weaker binding mode (formation constant around 106) is probably due to external loop binding. Evidence for the release of TMPyP4 upon protonation of bases at the loops has been observed. The results may be used for the design of porphyrin-based anti-cancer molecules with a higher affinity to G-quadruplex structures which may have anticancer properties. Protonation pushes away TMPyP4 molecules from the loops in G-quadruplex structures. The interaction of TMPyP4 porphyrin with the G-quadruplex structure formed by a guanine-rich sequence in the promoter region of c-kit gene was studied. Up to three ligand molecules may be bound to the G-quadruplex structure. Protonation at the loops induces the release of one TMPyP4 molecule. [Display omitted] ► Multivariate analysis and SPR were used to study the porphyrin–quadruplex interaction. ► The role of cytosine and adenine bases at the loops of G-quadruplex was studied. ► Two binding modes are shown with pH strongly influencing one of them.