Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry

• Published in: Nucleic acids research Vol. 38; no. 15; pp. 5217 - 5225
• Main Authors: Rosu, Frédéric, Gabelica, Valérie, Poncelet, Harmonie, De Pauw, Edwin
• Format: Journal Article Web Resource
• Language: English
• Published: England Oxford University Press 01-08-2010
• Subjects: Ammonium; Ammonium acetate; Biochemistry, biophysics & molecular biology; Biochimie, biophysique & biologie moléculaire; Cations; Chemistry; Chimie; Conformation; DNA; Evolution; g-quadruplex; G-Quadruplexes; Guanine; Ions; Kinetics; Life sciences; mass spectrometry; Mass spectroscopy; Methanol; Methanol - chemistry; Mobility; Monomers; noncovalent; Oligodeoxyribonucleotides - chemistry; Oligonucleotides; Physical, chemical, mathematical & earth Sciences; Physique, chimie, mathématiques & sciences de la terre; quadruplex; Sciences du vivant; self-assembly; Spectrometry; Spectrometry, Mass, Electrospray Ionization; Structural Biology
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkq208

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.