1l0r
From Proteopedia
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NMR Solution Structure of Nogalamycin Intercalation Between Co-Axially Stacked Hairpins
Overview
Two DNA hairpin motifs (5'-GCGAAGC-3' and 5'-ACGA AGT-3'), both stabilized, by a 5'-GAA loop, have been used to design novel intramolecular double, hairpin structures (5'-GCGAAGCACGAAGT-3' and 5'-ACGAAGTGCG AAGC-3') in, which coaxial stacking of the two hairpin components generates a, double-stranded stem region effectively with a single-strand break in the, middle of the sequence at either the TG or CA step between unconnected 3', and 5' terminal bases. We have investigated by NMR the conformation and, dynamics of the DNA at the strand break site. We show that mutual stacking, significantly enhances the stability of each hairpin. Further, the, anthracycline antibiotic nogalamycin binds cleanly to the 5'-TG (5'-CA), site formed by the mutually stacked hairpins despite the break in the, sugar-phosphate backbone on one strand. The complex resembles the, structure of nogalamycin-DNA complexes with the drug bound at 5'-TG sites, in intact duplex sequences, with pi-stacking interactions probably the, single dominant stabilizing interaction.
About this Structure
1L0R is a Protein complex structure of sequences from [1] with NA and NGP as ligands. Full crystallographic information is available from OCA.
Reference
Drug recognition of a DNA single strand break: nogalamycin intercalation between coaxially stacked hairpins., Williams HE, Colgrave ML, Searle MS, Eur J Biochem. 2002 Mar;269(6):1726-33. PMID:11895443
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