Fluorine‐Mediated Editing of a G‐Quadruplex Folding Pathway

Abstract

A (3+1)-hybrid-type G-quadruplex was substituted within its central tetrad by a single 2'-fluoro-modified guanosine. Driven by the anti-favoring nucleoside analogue, a novel quadruplex fold with inversion of a single G-tract and conversion of a propeller loop into a lateral loop emerges. In addition, scalar couplings across hydrogen bonds demonstrate the formation of intra- and inter-residual F⋅⋅⋅H8-C8 pseudo-hydrogen bonds within the modified quadruplexes. Alternative folding can be rationalized by the impact of fluorine on intermediate species on the basis of a kinetic partitioning mechanism. Apparently, chemical or other environmental perturbations are able to redirect folding of a quadruplex, possibly modulating its regulatory role in physiological processes.

Sugar Puckering Drives G‐Quadruplex Refolding: Implications for V‐Shaped Loops

“…Substituting two or three syn ‐residues in the 5′‐tetrad with F rG, rG, or F araG caused a reversal of the tetrad polarity under conservation of the global quadruplex fold . On the other hand, incorporating F rG or F araG into the single syn ‐position of the central tetrad lead to partial refolding into an antiparallel topology associated with an inversion of the first G‐tract and of the central tetrad polarity . In both cases, anti ‐favoring G analogues had very similar overall effects and differences were only observed in relative thermal stabilities and local structure, e.g., position‐dependent sugar conformations and participation of the 2′‐substituent in pseudo‐hydrogen bonds.…”

Manipulating DNA G‐Quadruplex Structures by Using Guanosine Analogues

“…Thus, the expected participation of fluorine in a sequential hydrogen bond to H8 was not observed when F rG was incorporated into the 5′‐tetrad of the ODN quadruplex, yet an O2′ ⋅⋅⋅ H8−C8 interaction was found for corresponding rG modifications (Figure B) . Moreover, whereas the anti F araG residue showed an intraresidue hydrogen bond when incorporated into central or outer positions of the ODN G4, a sequential F2′ ⋅⋅⋅ H8−C8 pseudo‐hydrogen bond was proposed on the basis of a high‐resolution NMR structure of an F araG‐modified two‐repeat telomeric quadruplex with a parallel fold (Figure C) . The dimeric structure also revealed a close contact between H2“ and O4′ of the 3′‐neighboring guanosine residue, indicating an additional stabilizing F2′−C2′−H2” ⋅⋅⋅ O4′ interaction.…”

“…Partial refolding of the (3+1)‐hybrid quadruplex ODN when substituted at a single syn position within its central tetrad by an F rG or F araG analogue was recently observed and characterized in detail . For both modified sequences two species coexist in solution: the native fold and a new topology with an inverted first G‐tract (Scheme ).…”

“…In contrast with tetrad polarity isomers, no dynamic equilibrium between the native and rearranged structure was observed, and their mutual interconversion requires complete strand separation. In support of a kinetic partitioning mechanism, the rather unusual substitution‐induced refolding can be traced to a stabilization of alternate G‐triplex intermediates, by taking account of the glycosidic torsion angle propensities of the G analogue and more favorable stacking interactions for anti – anti and syn – anti nucleotide steps along the G‐tracts …”

“…Remarkably, the coexistence of two stable quadruplex structures with either an anti or a syn conformation for 2′‐F‐modified G incorporated into the central tetrad of the ODN G4 illustrates that both F rG and F araG might also assume the disfavored syn glycosidic torsion angle in a conserved topology. Several examples suggest that the stability of different conformations both for 2′‐F‐ and for 2′‐OH‐substituted G analogues, which might possibly determine distinct global conformational rearrangements, seems to be partially linked to the formation of stabilizing unconventional hydrogen bonds between the 2′‐substituent in an S ‐puckered ribose unit as hydrogen bond acceptor and guanine C8−H8 (Figure ) . Strikingly, in the two coexisting ODN topologies with a single modification in the central tetrad (Scheme ), both syn F rG and syn F araG in the native G4, but also anti F rG in the rearranged G4, participate in a sequential F2′ ⋅⋅⋅ H8−C8 hydrogen bond to the 3′‐adjacent guanine base .…”