Purpose: A repeated, non-coding, DNA sequence d(TTAGGG)(n) is present in the telomeric ends of all human chromosomes. These repeats can adopt multiple inter- and intra-molecular non-B-DNA conformations that may play an important role in biological processes. We applied (125)I -radioprobing to assess the conformation of the human telomeric DNA fragment in a complex with the quadruplex-specific drug - cationic porphyrin TMPyP4.
Material and methods: Synthetic DNA oligonucleotides containing the telomeric sequence were labeled with (125)I. The probability of DNA breaks caused by decay of (125)I is inversely related to the distance between the radionuclide and the sugar unit of the DNA backbone; hence, the conformation of the DNA backbone can be deduced from the distribution of breaks.
Results: The obtained data indicate that the telomeric oligonucleotides predominantly fold into an intramolecular quadruplex conformation in the presence of TMPyP4. We propose a mixed-type (3 + 1) conformation of telomeric quadruplex in a complex with the cationic porphyrin TMPyP4 in solution. Binding of the porphyrin overrides the counterion effect on quadruplex conformation.
Conclusions: We have demonstrated that (125)I radioprobing can be successfully applied not only to determine folding in G-quadruplexes, but also to reveal the mode of quadruplex interaction with small ligands.