Impact of a Single Nucleotide Change or Non-Nucleoside Modifications in G-Rich Region on the Quadruplex-Duplex Hybrid Formation.

Dorota Gudanis,Zofia Gdaniec,Piotr Kozłowski,Ryszard Kierzek,Daniel Baranowski,Karolina Zielińska

doi:10.3390/biom11081236

Abstract

In this paper, a method to discriminate between two target RNA sequences that differ by one nucleotide only is presented. The method relies on the formation of alternative structures, i.e., quadruplex–duplex hybrid (QDH) and duplex with dangling ends (Dss), after hybridization of DNA or RNA G-rich oligonucleotides with target sequences containing 5′–GGGCUGG–3′ or 5′–GGGCGGG–3′ fragments. Using biophysical methods, we studied the effect of oligonucleotide types (DNA, RNA), non-nucleotide modifications (aliphatic linkers or abasic), and covalently attached G4 ligand on the ability of G-rich oligonucleotides to assemble a G-quadruplex motif. We demonstrated that all examined non-nucleotide modifications could mimic the external loops in the G-quadruplex domain of QDH structures without affecting their stability. Additionally, some modifications, in particular the presence of two abasic residues in the G-rich oligonucleotide, can induce the formation of non-canonical QDH instead of the Dss structure upon hybridization to a target sequence containing the GGGCUGG motif. Our results offer new insight into the sequential requirements for the formation of G-quadruplexes and provide important data on the effects of non-nucleotide modifications on G-quadruplex formation.

Highlights

It relies on the formation of alternative structures, i.e., a quadruplex–duplex hybrid (QDH) or duplex with long dangling ends (Dss) (Figure 1D,E), after the binding of G-rich oligonucleotides (Figure 1A) to target sequences that differ by a single U/G change (Figure 1B,C)
RNA sequences, GT and UT, that differ in one nucleotide only, based on the formation of alternative structures, i.e., quadruplex–duplex hybrids or duplexes with dangling ends, respectively
We designed DNA and RNA G-rich oligonucleotides with the ability to trigger the formation of a G-quadruplex motif only when hybridized to the GT target and leaving an unstructured G-rich fragment when hybridized to the UT sequence

Summary

Introduction

Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. In addition to the well-known double helix, nucleic acids can form a variety of different conformations. G-quadruplexes (G4) are structures that have received significant attention in recent years. The canonical, unimolecular G4 structures are formed from DNA or RNA

Results

Discussion

Conclusion