First Tandem Repeat of a Potassium Channel KCNN4 Minisatellite Folds into a V-Loop G-Quadruplex Structure

Na+-concentration dependent conformational switch of oncogene RET G-quadruplex DNA in solution

Proto-oncogene RET is overexpressed in many cancers, and its expression level is positively related to the size and malignancy of the tumors. Effective inhibition of its overexpression can be used to potentially treat cancers. A guanine-rich GC-boxes (I-V) sequence in its promoter region folds into noncanonical G-quadruplex (G4) DNA structures, negatively regulating its expression by interactions with small molecules. Previously, we reported that RET20T in GC-boxes II-V formed parallel G4 only at low concentrations of K+ solutions, and that RET-21mer in GC-boxes I-IV folded into different mixed parallel / antiparallel G4s in 50 mM K+ or 100 mM Na+ solutions. These data implied high complexity in producing G4 topology by cation type. Here, mainly by nuclear magnetic resonance (NMR), we demonstrated that RET20T formed slightly different, but rarely reported inter-convertible mixed parallel / antiparallel G4s dependent on Na+ concentration. Unclassical base-pairs G3•G6 and G14•T20 and ternary plane G3•C5•G6 stabilized these two RET20T G4 structures. These structural evidences enhanced our understanding that generation of a unimolecular G4 structure could be significantly affected by cation concentration and type in buffer, and the oligo sequence. Conformational switch of G4s should be noted before anti-cancer drug screening in future.

Showcasing Different G-Quadruplex Folds of a G-Rich Sequence: Between Rule-Based Prediction and Butterfly Effect

In better understanding the interactions of G-quadruplexes in a cellular or noncellular environment, a reliable sequence-based prediction of their three-dimensional fold would be extremely useful, yet is often limited by their remarkable structural diversity. A G-rich sequence related to a promoter sequence of the PDGFR-β nuclease hypersensitivity element (NHE) comprises a G3-G3-G2-G4-G3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical G-quadruplexes with uninterrupted G-columns can be expected, minimal base substitutions in a non-G-tract domain were shown to guide folding into either a basket-type antiparallel quadruplex, a parallel-stranded quadruplex with an interrupted G-column, a quadruplex with a V-shaped loop, or a (3+1) hybrid quadruplex. A 3D NMR structure for each of the different folds was determined. Supported by thermodynamic profiling on additional sequence variants, formed topologies were rationalized by the identification and assessment of specific critical interactions of loop and overhang residues, giving valuable insights into their contribution to favor a particular conformer. The variability of such tertiary interactions, together with only small differences in quadruplex free energies, emphasizes current limits for a reliable sequence-dependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.