CGG repeats associated with fragile X chromosome form left-handed Z-DNA structure

Abstract

This work is a continuation of our effort to determine the structure responsible for expansion of the (CGG)(n) motif that results in fragile X chromosome syndrome. In our previous report, we demonstrated that the structure adopted by an oligonucleotide with this repeat sequence is not a quadruplex as was suggested by others. Here we demonstrate that (CGG) runs adopt another anomalous arrangement-a left-handed Z-DNA structure. The Z-DNA formation was induced by high salt and millimolar concentrations of Ni(2+) ions and likelihood of its formation increased with increasing number of repeats. In an oligonucleotide in which the CGG runs were interrupted by AGG triplets, as is observed in genomes of healthy individuals, the hairpin conformation was stabilized and Z-DNA formation was hindered. We show here that methylation of the (CGG) runs markedly stabilized Z-DNA formation. We hypothesize that rather than in the expansion process the Z-DNA may be formed by long, expanded (CGG) stretches that become hypermethylated; this would inhibit transcription resulting in disease.

Circular Dichroism Spectroscopy of DNA: From Duplexes to Quadruplexes

“…This was the first proof of the Watson-Crick model, which was questioned at that time. [22][23][24] RNA is also able to transform into the left-handed structure, 25 and the A-Z switch may be linked to its function. 3) or in a combination of salt and alcohol.…”

On the sequence-directed nature of human gene mutation: The role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

“…A tenth polyalanine expansion disorder associated with the Zic family member 3 gene [ ZIC3 ; MIM# 300265] and leading to X-linked heterotaxy with VACTERL association has recently been described [Wessels et al, 2010]. Most of these microsatellite sequences have been shown to be capable of adopting specific secondary structures (non-B DNA), including hairpin-loops, three-(triplex) and four-stranded (quadruplex) structures and left-handed Z-DNA [Lopez Castel et al, 2010; Mirkin, 2007; Renciuk et al, 2011; Wells and Ashizawa, 2006]. Below, we review some of the most compelling evidence in support of a role for DNA secondary structures in either microsatellite expansion and/or the process of pathogenesis.…”

“…However, the mechanisms by which expanded (CGG•CCG) repeats induce methylation remain unclear. (CGG•CCG) repeats have been shown to fold into hairpin-loops [Amrane and Mergny, 2006; Darlow and Leach, 1998], quadruplexes [Khateb et al, 2004; Usdin and Woodford, 1995], left-handed Z-DNA [Renciuk et al, 2011], to possess inherently high flexibility (bending) [Bacolla et al, 1997] and are predicted to sustain stable ‘bubbles’ despite their high CG content [Alexandrov et al, 2011]. In vitro , the ability of DNA methyltransferase 1 (DNMT1) to methylate (CGG•CCG) repeats increases with increasing negative supercoiling [Bacolla et al, 2001].…”

Expansion of Microsatellites on Evolutionary Young Y Chromosome

“…Many microsatellite motifs can adopt unusual DNA conformations such as hairpins, quadruplexes, parallel duplexes and even left-handed Z-DNA [8]–[10]. Several decades ago it was shown that poly(dC-dA).poly(dT-dG) motifs can adopt a Z-DNA conformation [11].…”