Iodine-125 radioprobing of intramolecular quadruplex conformation of human telomeric DNA in the presence of cationic porphyrin TMPyP4

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 ¹²⁵I -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 ¹²⁵I. The probability of DNA breaks caused by decay of ¹²⁵I 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 ¹²⁵I 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.