Spectroscopic Characterization of Mitochondrial G-Quadruplexes.

Sara Illodo,Cibrán Pérez-González,Flor Rodríguez-Prieto,Mercedes Novo,Wajih Al-Soufi,Ramiro Barcia

doi:10.3390/ijms23020925

Abstract

Guanine quadruplexes (G4s) are highly polymorphic four-stranded structures formed within guanine-rich DNA and RNA sequences that play a crucial role in biological processes. The recent discovery of the first G4 structures within mitochondrial DNA has led to a small revolution in the field. In particular, the G-rich conserved sequence block II (CSB II) can form different types of G4s that are thought to play a crucial role in replication. In this study, we decipher the most relevant G4 structures that can be formed within CSB II: RNA G4 at the RNA transcript, DNA G4 within the non-transcribed strand and DNA:RNA hybrid between the RNA transcript and the non-transcribed strand. We show that the more abundant, but unexplored, G6AG7 (37%) and G6AG8 (35%) sequences in CSB II yield more stable G4s than the less profuse G5AG7 sequence. Moreover, the existence of a guanine located 1 bp upstream promotes G4 formation. In all cases, parallel G4s are formed, but their topology changes from a less ordered to a highly ordered G4 when adding small amounts of potassium or sodium cations. Circular dichroism was used due to discriminate different conformations and topologies of nucleic acids and was complemented with gel electrophoresis and fluorescence spectroscopy studies.

Highlights

The discovery of the DNA double helix structure in 1953 led to an enormous growth in our understanding of nucleic acids and their biological functions
Specific DNA sequences can display a number of different conformations, such as i-motif structures, hairpins and especially guanine quadruplexes, which have gained the attention of many researchers due to the recent evidence of their important biological implications
Following the folding topologies described by Karsisiotis and collaborators, we propose that, in the absence of cations, GCG6AG7 forms a less ordered, parallel G4 with looping sequence (−p−p−p+p) (Figure 4C), which reorganizes in the presence of the cations, yielding a highly ordered, more stable G4 of topology −(ppp) (Figure 4D)

Summary

Introduction

The discovery of the DNA double helix structure in 1953 led to an enormous growth in our understanding of nucleic acids and their biological functions. DNA does display single- or double-stranded structures [1,2]. Conformations, such as Holliday junctions, replication forks and DNA flaps, are formed during DNA replication, recombination and repair processes. Specific DNA sequences can display a number of different conformations, such as i-motif structures, hairpins and especially guanine quadruplexes, which have gained the attention of many researchers due to the recent evidence of their important biological implications. G4s appear on single stranded DNA and RNA guanine-rich regions, forming a highly polymorphic four-stranded structure. The G-quartet, is a square planar assembly of four guanines that forms Hoogsteen hydrogen bonds (Figure 1A) [3–6]

Methods

Results

Conclusion