High-resolution AFM structure of DNA G-wires in aqueous solution

Krishnashish Bose,Christopher J Lech,Anh Tuân Phan,Brahim Heddi

doi:10.1038/s41467-018-04016-y

Abstract

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface. A minor species shows primarily left-handed periodic features of 2.2 nm. In addition to 4.3 and 2.2 nm ridges, background features with periodicity of 0.9 nm are also observed. Using molecular modeling and simulation, we identify a molecular structure that can explain both the periodicity and handedness of the major G-wire species. Our results demonstrate the potential structural diversity of G-wire formation and provide valuable insight into the structure of higher-order intermolecular G-quadruplexes. Our results also demonstrate how AFM can be combined with simulation to gain insight into biomolecular structure.

Highlights

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM)
In 1994, Marsh et al.[41] proposed a model for G-wires formed by d[G4T2G4], in which two adjacent strands slip and overlap to form four-layer interlocked G-quadruplexes, which we refer to as the "(2,2) Adjacent" arrangement
We demonstrate that a slipped-strand model can give rise to the surface features observed in experimental AFM data

Summary

Introduction

We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4T2G4] in physiologically relevant aqueous solution using atomic force microscopy (AFM). The Tetrahymena telomeric sequence d[G4T2G4] was one of the first reported sequences known to self-assemble into wire-like structures, termed as G-wires, as visualized by dry atomic force microscopy (AFM) imaging on mica[11]. We report high-resolution AFM images of G-wires in an ionic aqueous environment and focus on the Tetrahymena telomeric DNA sequence d[G4T2G4], which has been extensively studied in the context of G-wire formation. We used AFM to probe higher-order structures formed by the self-assembly of the oligonucleotide d[G4T2G4] in aqueous solution. A large dataset of high-resolution AFM images enabled classification of G-wire diversity bas ed on height, periodicity, and handedness of the surface features. At 95 °C, the intensity of the 260 nm peak was reduced by only ~ 30% as compared with that at 25 °C (Supplementary Fig. 2), indicating that a significant fraction of the parallel G-quadruplex structures formed by d[G4T2G4], remained stable at high temperature (95 oC)

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Conclusion