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Structural Insights into the Quadruplex–Duplex 3′ Interface Formed from a Telomeric Repeat: A Potential Molecular Target

DOI: 10.1021/jacs.5b10492 DOI Help
PMID: 26730610 PMID Help

Authors: Irene Russo Krauss (University College London (UCL)) , Sneha Ramaswamy (University College London) , Stephen Neidle (University College London) , Shozeb Haider (University College London) , Gary Parkinson (University of London)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of The American Chemical Society , VOL 138 (4)

State: Published (Approved)
Published: January 2016

Abstract: We report here on an X-ray crystallographic and molecular modeling investigation into the complex 3′ interface formed between putative parallel stranded G-quadruplexes and a duplex DNA sequence constructed from the human telomeric repeat sequence TTAGGG. Our crystallographic approach provides a detailed snapshot of a telomeric 3′ quadruplex–duplex junction: a junction that appears to have the potential to form a unique molecular target for small molecule binding and interference with telomere-related functions. This unique target is particularly relevant as current high-affinity compounds that bind putative G-quadruplex forming sequences only rarely have a high degree of selectivity for a particular quadruplex. Here DNA junctions were assembled using different putative quadruplex-forming scaffolds linked at the 3′ end to a telomeric duplex sequence and annealed to a complementary strand. We successfully generated a series of G-quadruplex–duplex containing crystals, both alone and in the presence of ligands. The structures demonstrate the formation of a parallel folded G-quadruplex and a B-form duplex DNA stacked coaxially. Most strikingly, structural data reveals the consistent formation of a TAT triad platform between the two motifs. This triad allows for a continuous stack of bases to link the quadruplex motif with the duplex region. For these crystal structures formed in the absence of ligands, the TAT triad interface occludes ligand binding at the 3′ quadruplex–duplex interface, in agreement with in silico docking predictions. However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface.

Subject Areas: Biology and Bio-materials

Instruments: I03-Macromolecular Crystallography , I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography

Added On: 28/01/2016 13:25

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