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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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(A) Normalized UV melting profiles of (AGG)4A at 295 nm, (B) normalized thermal differential spectra of (AGG)2A and (C) CD spectra of (AGG)2A at 25°C. All the spectra were recorded in the presence of 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8 (green), 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 (red) and 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8 (blue).
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Figure 1: (A) Normalized UV melting profiles of (AGG)4A at 295 nm, (B) normalized thermal differential spectra of (AGG)2A and (C) CD spectra of (AGG)2A at 25°C. All the spectra were recorded in the presence of 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8 (green), 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 (red) and 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8 (blue).

Mentions: The melting profiles of (AGG)2A and (AGG)4A obtained at 295 nm in the presence of 50 mM K+, 150 mM NH4+ or 150 mM Na+ were typical of G-quadruplexes, with a decrease of absorbance upon melting (Figure 1A, Supplementary Figure S1A and B) (47). The TDS of (AGG)2A and (AGG)4A shown in Supplementary Figure S2A and B, respectively, also display a negative band at 295 nm in all conditions and support G-quadruplex formation (48). All these profiles are similar, with the exception of the TDS of (AGG)2A obtained in the presence of sodium ions for which a slight shift of the band at ∼250 nm toward a higher wavelength was observed (Figure 1B).


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)

(A) Normalized UV melting profiles of (AGG)4A at 295 nm, (B) normalized thermal differential spectra of (AGG)2A and (C) CD spectra of (AGG)2A at 25°C. All the spectra were recorded in the presence of 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8 (green), 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 (red) and 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8 (blue).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: (A) Normalized UV melting profiles of (AGG)4A at 295 nm, (B) normalized thermal differential spectra of (AGG)2A and (C) CD spectra of (AGG)2A at 25°C. All the spectra were recorded in the presence of 50 mM KCl, 10 mM potassium phosphate and 0.1 mM EDTA, pH 6.8 (green), 150 mM NH4Cl, 10 mM Tris/HCl, 0.1 mM EDTA, pH 6.8 (red) and 150 mM NaCl, 10 mM sodium phosphate, 0.1 mM EDTA, pH 6.8 (blue).
Mentions: The melting profiles of (AGG)2A and (AGG)4A obtained at 295 nm in the presence of 50 mM K+, 150 mM NH4+ or 150 mM Na+ were typical of G-quadruplexes, with a decrease of absorbance upon melting (Figure 1A, Supplementary Figure S1A and B) (47). The TDS of (AGG)2A and (AGG)4A shown in Supplementary Figure S2A and B, respectively, also display a negative band at 295 nm in all conditions and support G-quadruplex formation (48). All these profiles are similar, with the exception of the TDS of (AGG)2A obtained in the presence of sodium ions for which a slight shift of the band at ∼250 nm toward a higher wavelength was observed (Figure 1B).

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