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

Abstract

In better understanding the interactions of Gquadruplexes 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 G 3 -G 3 -G 2 -G 4 -G 3 pattern of five G-runs with two to four G residues. Although the predominant formation of three-layered canonical Gquadruplexes 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 sequencedependent prediction of favored topologies from sequences with multiple irregularly positioned G-tracts.

A pH‐Responsive Topological Switch Based on a DNA Quadruplex‐Duplex Hybrid

“…Such a pattern of glycosidic bond angles with both homopolar and heteropolar tetrad stacking has more frequently been observed for an antiparallel topology in a potassium ion solution. [21][22][23] Based on these findings, the G-quadruplex is suggested to adopt a chairtype topology with a counter-clockwise lateral loop progression termed-(lll) according to the notation introduced by Webba da Silva. [24] In analogy to the bromo-substituted 32Br TelQD employed in a recent study and shown to fold into a single topology (Table 1), [19] a most downfield-shifted resonance at 14.34 ppm showing a strong NOE contact to A30 H2 can unambiguously be identified through a residue-specific 15 N-labeling to be an imino proton of N1-protonated residue A30 positioned within the third lateral loop (Figure S3).…”

“…Interestingly, formation of a (3 + 1) hybrid topology with a propeller, diagonal, and lateral loop has only rarely been observed. [21,28] Here, it may be a consequence of the hairpin sequence, forming a first propeller loop that prevents base pairing of its 5'-and 3'-terminal C and G residues now located at opposite faces of the G-core. [17] Rather than remaining unpaired, 3'-terminal G18 engages in a G-tetrad to release G21 in a register shift for participation in a sterically more relaxed 4nt diagonal loop.…”

Structural Basis for Parallel G-Quadruplex Recognition by an Ankyrin Protein

“…The core of a G4 structure is composed of a stack of multiple G-tetrads − stabilized by central cations, , such as K + or Na + . Studies over the last few decades have shed light on the polymorphism of G4s. − ,, G4 structures are commonly classified based on the strand polarity: (i) parallel or (4 + 0), where all four strands are in one direction; (ii) antiparallel or (2 + 2), where two pairs of strands are in opposite directions; (iii) hybrid or (3 + 1), where three strands run in one direction and the fourth strand runs in the opposite direction. A good example of G4 diversity is presented by the human telomeric sequences (TTAGGG) n .…”