Binding of anthracycline antibiotic nogalamycin to the site of a DNA single strand break engineered between two co-axially stacked hairpins

Abstract

We show by NMR that the DNA sequence 5′-GCGAAGCACGAAGT folds to form an intramolecular double hairpin structure containing 5′-GAA loops with co-axial stacking of the two hairpins significantly increasing their stability; the anthracycline antibiotic nogalamycin is able to intercalate between the two hairpins (5′-TG step) despite the break in the phosphodiester backbone.