Ethanol is a better inducer of DNA guanine tetraplexes than potassium cations

Vorlı́čková, Michaela; Bednářová, Klára; Kypr, Jaroslav

doi:10.1002/bip.20488

Cited by 44 publications

(42 citation statements)

References 44 publications

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“…The lefthanded form may also be induced as a consequence of methylation. The anomalous duplex structure with flipped out guanine bases (see Figure 5) may be analogous to the e-structure experimentally observed with the (CCG) 15 fragment. 39 Such a deformed structure was shown to be an ideal substrate for a methyltransferase.…”

Section: Discussionmentioning

confidence: 66%

“…We have, however, shown that (CGG) n fragments form quadruplexes only at low pH, 13 in the presence of very high KCl concentrations in aqueous solutions, 14 or in the presence of ethanol. 15,16 The ability to form quadruplex dramatically decreases with the (CGG) n fragment length. In addition, the (AGG) triplets that interrupt (CGG) runs in genomes of healthy individuals, significantly stabilized quadruplex formation in our model systems.…”

Section: Introductionmentioning

confidence: 99%

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

2010

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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.

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Section: Discussionmentioning

confidence: 66%

Section: Introductionmentioning

confidence: 99%

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

2010

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“…64 The results can be compared with those drawn from other single molecule detections. 65;66 Contributions from individual guanines to folding stability and the multi-step folding process in more complicated G-quadruplexes 32 may also be detected.…”

Section: Resultsmentioning

confidence: 99%

Encapsulating a Single G-Quadruplex Aptamer in a Protein Nanocavity

Shim

2008

J. Phys. Chem. B

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The α-hemolysin (αHL) protein pore has many applications in biotechnology. This article describes a single-molecule manipulation system that utilizes the nanocavity enclosed by this pore to noncovalently encapsulate a guest molecule. The guest is the thrombin-binding aptamer (TBA) that folds into the G-quadruplex in the presence of cations. Trapping the G-quadruplex in the nanocavity resulted in characteristic changes to the pore conductance that revealed important molecular processes, including spontaneous unfolding of the quartet structure and translocation of unfolded DNA in the pore. Through detection with tag-TBA, we localized the G-quadruplex near the entry of the β-barrel inside the nanocavity, where the molecule vibrates and rotates to different orientations. This guest-nanocavity supramolecular system has potential for helping to understand singlemolecule folding and unfolding kinetics.

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“…Unfortunately, these rules are based solely on NMR, which does not determine the number of associated strands directly. According to our studies, 28 intramolecular guanine quadruplexes containing only two guanine tetrads are rarely formed. That is why we have chosen oligonucleotides for the present study capable of forming three guanine tetrads.…”

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confidence: 90%

Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions

et al. 2007

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DNA guanine quadruplexes are all based on stacks of guanine tetrads, but they can be of many types differing by mutual strand orientation, topology, position and structure of loops, and the number of DNA molecules constituting their structure. Here we have studied a series of nine DNA fragments (G(3)Xn)(3)G(3), where X = A, C or T, and n = 1, 2 or 3, to find how the particular bases and their numbers enable folding of the molecule into quadruplex and what type of quadruplex is formed. We show that any single base between G(3) blocks gives rise to only four-molecular parallel-stranded quadruplexes in water solutions. In contrast to previous models, even two Ts in potential loops lead to tetramolecular parallel quadruplexes and only three consecutive Ts lead to an intramolecular quadruplex, which is antiparallel. Adenines make the DNA less prone to quadruplex formation. (G(3)A(2))(3)G(3) folds into an intramolecular antiparallel quadruplex. The same is true with (G(3)A(3))(3)G(3) but only in KCl. In NaCl or LiCl, (G(3)A(3))(3)G(3) prefers to generate homoduplexes. Cytosine still more interferes with the quadruplex, which only is generated by (G(3)C)(3)G(3), whereas (G(3)C(2))(3)G(3) and (G(3)C(3))(3)G(3) generate hairpins and/or homoduplexes. Ethanol is a more potent DNA guanine quadruplex inducer than are ions in water solutions. It promotes intramolecular folding and parallel orientation of quadruplex strands, which rather corresponds to quadruplex structures observed in crystals.

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Ethanol is a better inducer of DNA guanine tetraplexes than potassium cations

Cited by 44 publications

References 44 publications

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

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

Encapsulating a Single G-Quadruplex Aptamer in a Protein Nanocavity

Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions

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