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Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats.

Malgowska M, Gudanis D, Kierzek R, Wyszko E, Gabelica V, Gdaniec Z - Nucleic Acids Res. (2014)

Bottom Line: We also found that each G-quadruplex fold is different: A:(G:G:G:G)A hexads were found for (AGG)2A, whereas mixed G:C:G:C tetrads and U-tetrads were observed in the NMR spectra of G(CGG)2C and p(UGG)2U, respectively.Finally, our NMR study highlights the influence of the strand sequence on the structure formed, and the influence of the intracellular environment on the folding.Importantly, we highlight that although potassium ions are prevalent in cells, the structures observed in the HeLa cell extract are not always the same as those prevailing in biophysical studies in the presence of K(+) ions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland.

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Imino regions of the 1H NMR spectra of (A) G(CGG)2C and (B) G(CGG)4C at 10°C in the presence of (Aa, Ba, Ad, Bd) 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8, (Ab, Bb) 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8, (Ac, Bc) 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 and (Ae, Be) HeLa cell extract. The poor S/N ratio observed for G(CGG)4C is due to polymorphism or/and the presence of higher order structures.
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Figure 5: Imino regions of the 1H NMR spectra of (A) G(CGG)2C and (B) G(CGG)4C at 10°C in the presence of (Aa, Ba, Ad, Bd) 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8, (Ab, Bb) 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8, (Ac, Bc) 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 and (Ae, Be) HeLa cell extract. The poor S/N ratio observed for G(CGG)4C is due to polymorphism or/and the presence of higher order structures.

Mentions: Figure 5Aa represents an 1H NMR spectrum of G(CGG)2C in the presence of K+ ions. In these conditions, four imino resonances appear in the region distinctive of G-quadruplex structures and one guanosine imino proton resonates at 12.44 ppm, a region characteristic of Watson–Crick G·C base pairs. It has been previously demonstrated that the presence of 5′-GC ends can lead to the association of two G-quadruplex moieties through G·C base pairs and the formation of two G:C:G:C-tetrads (54). Overall, the observation of the inverted UV melting profile at 295 nm and a negative band at this wavelength in the TDS spectrum, together with the analysis of the ESI-MS and 1H NMR spectra indicated the formation of a highly symmetric tetramolecular G-quadruplex structure with G:G:G:G and mixed G:C:G:C tetrads (Figure 4B, C and F) in the K+-containing solution.


Distinctive structural motifs of RNA G-quadruplexes composed of AGG, CGG and UGG trinucleotide repeats.

Malgowska M, Gudanis D, Kierzek R, Wyszko E, Gabelica V, Gdaniec Z - Nucleic Acids Res. (2014)

Imino regions of the 1H NMR spectra of (A) G(CGG)2C and (B) G(CGG)4C at 10°C in the presence of (Aa, Ba, Ad, Bd) 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8, (Ab, Bb) 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8, (Ac, Bc) 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 and (Ae, Be) HeLa cell extract. The poor S/N ratio observed for G(CGG)4C is due to polymorphism or/and the presence of higher order structures.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150804&req=5

Figure 5: Imino regions of the 1H NMR spectra of (A) G(CGG)2C and (B) G(CGG)4C at 10°C in the presence of (Aa, Ba, Ad, Bd) 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8, (Ab, Bb) 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8, (Ac, Bc) 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 and (Ae, Be) HeLa cell extract. The poor S/N ratio observed for G(CGG)4C is due to polymorphism or/and the presence of higher order structures.
Mentions: Figure 5Aa represents an 1H NMR spectrum of G(CGG)2C in the presence of K+ ions. In these conditions, four imino resonances appear in the region distinctive of G-quadruplex structures and one guanosine imino proton resonates at 12.44 ppm, a region characteristic of Watson–Crick G·C base pairs. It has been previously demonstrated that the presence of 5′-GC ends can lead to the association of two G-quadruplex moieties through G·C base pairs and the formation of two G:C:G:C-tetrads (54). Overall, the observation of the inverted UV melting profile at 295 nm and a negative band at this wavelength in the TDS spectrum, together with the analysis of the ESI-MS and 1H NMR spectra indicated the formation of a highly symmetric tetramolecular G-quadruplex structure with G:G:G:G and mixed G:C:G:C tetrads (Figure 4B, C and F) in the K+-containing solution.

Bottom Line: We also found that each G-quadruplex fold is different: A:(G:G:G:G)A hexads were found for (AGG)2A, whereas mixed G:C:G:C tetrads and U-tetrads were observed in the NMR spectra of G(CGG)2C and p(UGG)2U, respectively.Finally, our NMR study highlights the influence of the strand sequence on the structure formed, and the influence of the intracellular environment on the folding.Importantly, we highlight that although potassium ions are prevalent in cells, the structures observed in the HeLa cell extract are not always the same as those prevailing in biophysical studies in the presence of K(+) ions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland.

Show MeSH
Related in: MedlinePlus