Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences.

Sebastian L B König,Amanda C Evans,Julian L Huppert,Roland K O Sigel

doi:10.1093/nar/gkt476

Abstract

G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions.

Highlights

The canonical Watson–Crick (W–C) double-helix conformation of DNA has been extensively studied and is well understood
Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions
This research demonstrates that both G-quadruplex and i-motif substructures cause a distance-dependent destabilization of directly adjacent duplex DNA

Summary

Introduction

The canonical Watson–Crick (W–C) double-helix conformation of DNA has been extensively studied and is well understood. It is less well known that nucleic acids can form alternative conformational structures, such as G-quadruplexes and i-motifs. A G-quadruplex conformer consists of stacks of G-quartets, which are composed of four guanine bases arranged in a plane and stabilised by Hoogsteen (H) and W–C hydrogen-bonding interactions [1]. Enhanced electrostatic and p–p-bonding interactions cause these G-quartets to stack together into G-quadruplex conformers: this stacking has been found to be strongly favoured by the presence of mono- and divalent cations (Figure 1A) [2,3]. G-quadruplex stability in isolation has been thoroughly studied, and significant influencing factors include the number of stacked G-quartets, G-quadruplex topology and the type of G-quadruplexbinding cation present in solution [6,7,8,9,10,11]. A G-quadruplex is most likely to form in the presence of at least four consecutive G-runs; putative G-quadruplex-forming regions can be predicted by scanning through nucleic acid genetic sequences [12]

Methods

Results

Conclusion