title: 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.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Analytical Chemistry, University of Barcelona, Barcelona, Spain.
authors.forename: Sintayehu
authors.initials: S
authors.lastname: Manaye
authors.forename: Ramon
authors.initials: R
authors.lastname: Eritja
authors.forename: Anna
authors.initials: A
authors.lastname: Aviñó
authors.forename: Joaquim
authors.initials: J
authors.lastname: Jaumot
authors.forename: Raimundo
authors.initials: R
authors.lastname: Gargallo
mesh_terms: D054856:G-Quadruplexes; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D011166:Porphyrins / Q000378:metabolism*; D000090063:Proto-Oncogene Mas; D019009:Proto-Oncogene Proteins c-kit / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D013379:Substrate Specificity; D020349:Surface Plasmon Resonance; D014158:Transcription, Genetic; D015533:Transcriptional Activation
chemical_list: C000715470:MAS1 protein, human; D011166:Porphyrins; D000090063:Proto-Oncogene Mas; C021096:tetra(4-N-methylpyridyl)porphine; D019009:Proto-Oncogene Proteins c-kit