Interactions of small molecules with duplex DNA and lesion containing G-quadruplex DNA

The low redox potential of guanines (G 1.29 V vs. NHE) compared to other nucleobases, makes them potentially susceptible to attack by exogenous and endogenous damaging species. This property of guanine has also been utilized for the development of several anticancer agents including the well-known platinum complexes, cisplatin and carboplatin. The two closely related nickel complexes, NiCR and NiCR-2H, exhibit significant differences in cytotoxicity towards MCF-7 cancer cells. In the first part of this work, we explain this difference using biochemical and biophysical approaches to study their interactions with duplex DNA. The nickel complexes were found to selectively oxidize guanines in bulged DNA structures in the presence of oxidant and notably NiCR-2H oxidizes guanines more efficiently than NiCR. According to 1 H NMR studies, NiCR-2H binds strongly to the N7 position of dGMP compared to NiCR and could be an important oxidation product of NiCR under physiological conditions. The second part of this work focuses on the secondary DNA structures known as G-quadruplex formed in the guanine rich telomeric region. G-quadruplex is formed by stacking of G-quartets (a coplanar cyclic array of four Gs) on top of each other. Its formation is known to inhibit the activity of the reverse transcriptase telomerase that is overexpressed in 80-90% cancer cells. The guanines in telomeric DNA are readily oxidized due to their low redox potential and the major oxidation product is 7, 8-dihydro-8-oxoguanine (OxodG). OxodG (0.58 V vs. NHE) can further be oxidized in the presence of one electron oxidants and the resulting product forms adducts with endogenous nucleophiles such as spermine. In light of these findings, we hereby designed and synthesized novel bifunctional perylene derivatives that can selectively bind to the telomeric DNA via G-quadruplex formation and subsequently react with OxodG in close proximity. These compounds have strong binding affinity towards G-quadruplex and can significantly stabilize the OxodG containing G-quadruplex motif by end stacking on the upper G-quartet. The effect of these compounds on telomerase activity and cytotoxicity towards Hep3B cancer cells was also evaluated