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Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry.

Rosu F, Gabelica V, Poncelet H, De Pauw E - Nucleic Acids Res. (2010)

Bottom Line: 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.We also show that the addition of methanol to the monomer solution significantly accelerates the cation-induced G-quadruplex assembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry B6c, University of Liège, Liège, Belgium. f.rosu@ulg.ac.be

ABSTRACT
Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, 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 degrees 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.

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(a) Structure of a guanine quartet (or G-quartet), (b) the perfectly aligned tetramolecular G-quadruplex formed by the oligonucleotide dTG5T contains five G-quartets and four ammonium ions, (c) a tetramolecular G-quadruplex with one strand slipped by one base contains four G-quartets and three ammonium ions.
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Figure 1: (a) Structure of a guanine quartet (or G-quartet), (b) the perfectly aligned tetramolecular G-quadruplex formed by the oligonucleotide dTG5T contains five G-quartets and four ammonium ions, (c) a tetramolecular G-quadruplex with one strand slipped by one base contains four G-quartets and three ammonium ions.

Mentions: G-quadruplexes encompass all nucleic acid structures involving the G-quartet motif (Figure 1a), in which four guanines are assembled in a square planar structure by Hoogsteen hydrogen bonds (1,2). G-quadruplexes can be formed by biologically relevant DNA and RNA sequences (3–6), and by synthetic G-rich nucleic acid strands. Tetramolecular G-quadruplexes constituted from four identical strands arranged in parallel orientation have been extensively studied (7,8), because they constitute a model for G-quadruplex structure, formation and interaction with small molecules. Furthermore, intermolecular G-quadruplexes are also a particularly interesting scaffold for the design of artificial nanostructures (1,9–11), owing to their stability, rigidity and electronic properties (12,13). Several synthetic quadruplex-forming oligonucleotides, either dimeric (14–16) or tetrameric (17,18), have been reported for their therapeutic properties, such as anti-cancer (19) or anti-HIV (15–17,20) treatment.Figure 1.


Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry.

Rosu F, Gabelica V, Poncelet H, De Pauw E - Nucleic Acids Res. (2010)

(a) Structure of a guanine quartet (or G-quartet), (b) the perfectly aligned tetramolecular G-quadruplex formed by the oligonucleotide dTG5T contains five G-quartets and four ammonium ions, (c) a tetramolecular G-quadruplex with one strand slipped by one base contains four G-quartets and three ammonium ions.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2926595&req=5

Figure 1: (a) Structure of a guanine quartet (or G-quartet), (b) the perfectly aligned tetramolecular G-quadruplex formed by the oligonucleotide dTG5T contains five G-quartets and four ammonium ions, (c) a tetramolecular G-quadruplex with one strand slipped by one base contains four G-quartets and three ammonium ions.
Mentions: G-quadruplexes encompass all nucleic acid structures involving the G-quartet motif (Figure 1a), in which four guanines are assembled in a square planar structure by Hoogsteen hydrogen bonds (1,2). G-quadruplexes can be formed by biologically relevant DNA and RNA sequences (3–6), and by synthetic G-rich nucleic acid strands. Tetramolecular G-quadruplexes constituted from four identical strands arranged in parallel orientation have been extensively studied (7,8), because they constitute a model for G-quadruplex structure, formation and interaction with small molecules. Furthermore, intermolecular G-quadruplexes are also a particularly interesting scaffold for the design of artificial nanostructures (1,9–11), owing to their stability, rigidity and electronic properties (12,13). Several synthetic quadruplex-forming oligonucleotides, either dimeric (14–16) or tetrameric (17,18), have been reported for their therapeutic properties, such as anti-cancer (19) or anti-HIV (15–17,20) treatment.Figure 1.

Bottom Line: 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.We also show that the addition of methanol to the monomer solution significantly accelerates the cation-induced G-quadruplex assembly.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry B6c, University of Liège, Liège, Belgium. f.rosu@ulg.ac.be

ABSTRACT
Electrospray mass spectrometry was used to investigate the mechanism of tetramolecular G-quadruplex formation by the DNA oligonucleotide dTG(5)T, 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 degrees 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.

Show MeSH
Related in: MedlinePlus