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

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.

A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs

“…length and flexibility of the linker, as well as the attachment points onto both ligands) and might not apply between different quadruplex-duplex hybrid systems. On a separate note, the duplex-quadruplex junction can also serve as a unique recognition site by a junction binder 33 , 51 , 52 , which can be applied independently or in combination with the duplex- and quadruplex-binding ligands.…”

Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex

“…Previous biophysical stability studies indicate that formation of G4 and i-motif conformations do destabilize proximal duplex DNA structures ( 59 ). On the other side, addition of 3′ or 5′ nucleotides to G4 sequences also strongly affects the folding conformation and stability of G4s as assessed by NMR, UV-spectroscopy and CD ( 15 , 16 , 60 , 61 ). The influences of duplex DNA on G4 structure have been characterized by several studies.…”

2′-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA

“…While the presence of i-motif and G4 folds may be mutually exclusive under certain conditions, our results suggest that they may co-exist transiently as intermediates in telomeric sequences. Hybrid structures such as the ones studied here represent attractive tools for the discovery of selective ligands that can specifically stabilize i-motif structures, or target the G4/i-motif-duplex interface, which can in turn interfere with telomerase activity ( 61 , 62 ). In this context, 2′F-ANA modification may become a useful method for building stable supramolecular DNA nanostructures based on the co-existence of i-motif and G4 complexes ( 63 ), and for modulating the response of i-motif based nanodevices ( 64 , 65 ).…”