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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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Electrospray mass spectrum of (AGG)4A in the presence 150 mM ammonium acetate. The final single strand RNA concentration was 18 μM. 10% v/v of methanol was added 1 h before measurement. The peak annotation [n]z-­ indicates the number of strands (n) and the total charge (z). The distribution of the number of ammonium ions preserved in the structure is shown in the inset. The distribution is presented at three bias voltages.
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Figure 2: Electrospray mass spectrum of (AGG)4A in the presence 150 mM ammonium acetate. The final single strand RNA concentration was 18 μM. 10% v/v of methanol was added 1 h before measurement. The peak annotation [n]z-­ indicates the number of strands (n) and the total charge (z). The distribution of the number of ammonium ions preserved in the structure is shown in the inset. The distribution is presented at three bias voltages.

Mentions: We then established the molecularity of the G-quadruplexes as well as the number of the adducted ammonium ions preserved in the structure using negative ion mode ESI-MS. For parallel-stranded structures, ammonium ion preservation in the gas phase is easier than for antiparallel structures (42–44). As the structures formed here are parallel-stranded both in ammonium and in potassium, we are in a favourable case where the ammonium ion count by ESI-MS allows us to deduce the number of adjacent stacked tetrads. The ESI-MS spectrum of (AGG)2A shows two significant peaks (Supplementary Figure S4A). The peak at m/z 1151.86 corresponds to a monomer at charge state 2- without adducted ammonium ions, whereas the peak at m/z 1859.57 corresponds to the tetramolecular G-quadruplex structure at charge state 5- with three, four or five trapped ammonium ions. The distribution of ammonium ion adducts is presented in the insert of Supplementary Figure S4A. The ESI-MS spectrum of (AGG)4A is presented in Figure 2. Only one peak at m/z 1747.82 and charge state 5- was observed, corresponding to the bimolecular G-quadruplex structure stabilized by three ammonium ions, suggesting the contiguous stacking of four tetrads.


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)

Electrospray mass spectrum of (AGG)4A in the presence 150 mM ammonium acetate. The final single strand RNA concentration was 18 μM. 10% v/v of methanol was added 1 h before measurement. The peak annotation [n]z-­ indicates the number of strands (n) and the total charge (z). The distribution of the number of ammonium ions preserved in the structure is shown in the inset. The distribution is presented at three bias voltages.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 2: Electrospray mass spectrum of (AGG)4A in the presence 150 mM ammonium acetate. The final single strand RNA concentration was 18 μM. 10% v/v of methanol was added 1 h before measurement. The peak annotation [n]z-­ indicates the number of strands (n) and the total charge (z). The distribution of the number of ammonium ions preserved in the structure is shown in the inset. The distribution is presented at three bias voltages.
Mentions: We then established the molecularity of the G-quadruplexes as well as the number of the adducted ammonium ions preserved in the structure using negative ion mode ESI-MS. For parallel-stranded structures, ammonium ion preservation in the gas phase is easier than for antiparallel structures (42–44). As the structures formed here are parallel-stranded both in ammonium and in potassium, we are in a favourable case where the ammonium ion count by ESI-MS allows us to deduce the number of adjacent stacked tetrads. The ESI-MS spectrum of (AGG)2A shows two significant peaks (Supplementary Figure S4A). The peak at m/z 1151.86 corresponds to a monomer at charge state 2- without adducted ammonium ions, whereas the peak at m/z 1859.57 corresponds to the tetramolecular G-quadruplex structure at charge state 5- with three, four or five trapped ammonium ions. The distribution of ammonium ion adducts is presented in the insert of Supplementary Figure S4A. The ESI-MS spectrum of (AGG)4A is presented in Figure 2. Only one peak at m/z 1747.82 and charge state 5- was observed, corresponding to the bimolecular G-quadruplex structure stabilized by three ammonium ions, suggesting the contiguous stacking of four tetrads.

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