The Folding Landscapes of Human Telomeric RNA and DNA G-Quadruplexes are Markedly Different.

Diana Müller,Harald Schwalbe,Christian Richter,Irene Bessi

doi:10.1002/anie.202100280

Diana Müller, Harald Schwalbe + Show 2 more

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https://doi.org/10.1002/anie.202100280

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Abstract

We investigated the folding kinetics of G‐quadruplex (G4) structures by comparing the K+‐induced folding of an RNA G4 derived from the human telomeric repeat‐containing RNA (TERRA25) with a sequence homologous DNA G4 (wtTel25) using CD spectroscopy and real‐time NMR spectroscopy. While DNA G4 folding is biphasic, reveals kinetic partitioning and involves kinetically favoured off‐pathway intermediates, RNA G4 folding is faster and monophasic. The differences in kinetics are correlated to the differences in the folded conformations of RNA vs. DNA G4s, in particular with regard to the conformation around the glycosidic torsion angle χ that uniformly adopts anti conformations for RNA G4s and both, syn and anti conformation for DNA G4s. Modified DNA G4s with 19F bound to C2′ in arabino configuration adopt exclusively anti conformations for χ. These fluoro‐modified DNA (antiTel25) reveal faster folding kinetics and monomorphic conformations similar to RNA G4s, suggesting the correlation between folding kinetics and pathways with differences in χ angle preferences in DNA and RNA, respectively.

Highlights

G-quadruplexes (G4s) are four-stranded oligonucleotides formed both by RNA and DNA G-rich sequences that are stabilised through Hoogsteen hydrogen-bonds and binding to monovalent cations, in particular K+
Five anti-directing modifications were introduced in a 25mer DNA G4-forming sequence at positions with guanosines in syn conformation allowing us to drive the DNA structure from a hybrid towards a parallel G4 conformation as observed for RNA G4s
Replacing five deoxyguanosine residues was not sufficient to completely reshape the folding landscape from the typical DNA G4 folding landscape with kinetic partitioning to the RNA G4 funnel-like folding landscape

Summary

Introduction

G-quadruplexes (G4s) are four-stranded oligonucleotides formed both by RNA and DNA G-rich sequences that are stabilised through Hoogsteen hydrogen-bonds and binding to monovalent cations, in particular K+. DNA G4s are polymorphic and their structures differ in terms of strand orientation, conformation of the glycosidic torsion angle c (syn, c = 40–808, or anti, c = 180–2408) (Scheme 1) and geometry of loops connecting the G-rich tracts.[3]. The investigation reported here were motivated by the hypothesis that RNA G4 folding should be faster, since the change from the more stable anti conformation for unfolded guanosine nucleotides to the less stable syn conformation adopted in antiparallel or hybrid G4 architectures would not be required. By comparison with 19F-modified DNA in arabino configuration that adopts anti conformations, we provide evidence that these altered folding kinetics are linked to the conformation around the glycosidic bond angle c. In analogy to our previous investigations, the minor population of wtTel most likely adopts a hybrid-type structure but this has not been assigned so far.[4,19]

Results and Discussion

Conclusion

Conflict of interest