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See detailTetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry
Rosu, Frédéric ULg; Gabelica, Valérie ULg; Poncelet, Harmonie et al

in Nucleic Acids Research (2010)

Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG5T, in ammonium acetate. The intermediates and products were ... [more ▼]

Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG5T, in ammonium acetate. The intermediates and products were separated according to their mass (number of strands and inner cations) and quantified. The study of the temporal evolution of each species allows us to propose the following formation mechanism. (i) Monomers, dimers and trimers are present at equilibrium already in the absence of ammonium acetate. (ii) The addition of cations promotes the formation of tetramers and pentamers that incorporate ammonium ions and therefore presumably have stacked guanine quartets in their structure. (iii) The pentamers eventually disappear and tetramers become predominant. However, these tetramers do not have their four strands perfectly aligned to give five G-quartets: the structures contain one ammonium ion too few, and ion mobility spectrometry shows that their conformation is more extended. (iv) At 4°C, the rearrangement of the kinetically trapped tetramers with presumably slipped strand(s) into the perfect G-quadruplex structure is extremely slow (not complete after 4 months). We also show that the addition of methanol to the monomer solution significantly accelerates the cation-induced G-quadruplex assembly. [less ▲]

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Peer Reviewed
See detailExploring the Formation Pathways of DNA G-Quadruplex Architectures
Rosu, Frédéric ULg; Poncelet, Harmonie; Teulade-Fichou, Marie-Paule et al

Conference (2007, September 07)

Guanine-rich DNA strands can form the so-called G-quadruplex architectures due to the formation of quartets of guanines linked by 8 hydrogen bonds. G-quadruplexes are further stabilized by the inclusion ... [more ▼]

Guanine-rich DNA strands can form the so-called G-quadruplex architectures due to the formation of quartets of guanines linked by 8 hydrogen bonds. G-quadruplexes are further stabilized by the inclusion of cations between the G-quartets. The abundance of G-rich regions throughout the genome and their very presence in telomeric regions made G-quadruplexes interesting targets. NMR and crystallographic studies of G-quadruplex structures revealed amazing variety in the G-quadruplex topologies. The next challenge will be to understand the rules governing the formation of the various topologies, in order to predict relevant G-quadruplexes in the genome, and in order to act rationally on their formation or disruption. To date, only few experimental [1] or theoretical [2] studies have been devoted to investigating the mechanisms of G-quadruplex formation. We report here a detailed investigation of DNA G-quadruplex formation pathways using electrospray mass spectrometry (ESI-MS). The sequences TGnT (n = 3-6) were purchased from Eurogentec (Seraing, Beliugm). ESI-MS experiments were performed in the negative ion mode on a Q-TOF Ultima Global (Waters, Manchester, UK). The cation used was ammonium (up to 150 mM). Experiments were performed in the presence and absence of methanol (up to 20%) as co-solvent. ESI-MS allows counting both the number of strands and the number of cations in each intermediate. We could confirm the presence of transient dimer and trimer intermediates in low abundance. More unexpectedly, ESI-MS also reveals unambiguously the formation of pentamers which contain ammonium cations. The pentamers slowly convert into tetramers. Counting the number of included cations also revealed that, in the case of (TG6T)4, inclusion of four ammonium cations is fast, while the inclusion of the last ammonium ion is very slow. We also found that the addition of methanol (initially added to obtain higher ion intensities) significantly increases the rate of G-quadruplex formation. Finally, we also investigated the role of G-quadruplex ligands in the rate of formation of G-quadruplexes. We could classify the ligands according to their increase of G-quadruplex formation kinetics, and distinguish the intermediates. Interestingly, one ligand showed formation of a higher-order structure by bridging two G-quadruplexes. Acknowledgement: The authors thank the FRS-FNRS for their support. References: [1] J. Gros et al., Nucleic Acids Res., 2007, doi:10.1093/nar/gkm111. [2] R. Stefl et al., Biophys. J., 2003, 85(3), 1787-1804. [less ▲]

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