Bimolecular quadruplexes and their transitions to higher-order molecular structures detected by ESI-FTICR-MS

Abstract

Four individual quadruplexes, which are self-assembled in ammonium acetate solution from telomeric sequences of closely related DNA strands-d(G 4 T 4 G 4 ), d(G 3 T 4 G 4 ), d(G 3 T 4 G 3 ), and d(G 4 T 4 G 3 )-have been detected in the gas phase using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS). The bimolecular quadruplexes associate with the same number of NH 4 ϩ in the gas phase as NMR shows that they do in solution. The quadruplex structures formed in solution are maintained in the gas phase. Furthermore, the mass spectra show that the bimolecular quadruplexes generated by the strands d( Of particular interest is a telomeric DNA that consists of repeating sequences, such as TTAGGG in vertebrates and TTTTGGGG in Oxytricha. These sequences have been proven to fold into quadruplexes in vitro and potentially have the function of inhibiting telomerase activities. The telomerase, a reverse enzyme expressed in more than 80% of tumor cells, responds for the replication of the telomeric DNA and has been considered as a target for anticancer drug design [4,5]. Guanine-rich oligonucleotides can also self-associate into higher-order structures, such as supermolecular G-wires [6], which serve as artificial ion channels and ion receptors and which have a wide range of applications in medicine, materials science, and nanotechnology [2,7,8].DNA quadruplex structures can be formed from one, two, or four oligonucleotide strands and are stabilized by coordinated monovalent cations acting between adjacent G-quartets [1, 9 -11]. The strands with single repeating guanine sequences usually arrange themselves from the 5= to the 3= end in parallel four-stranded quadruplexes, whereas the strands with more than two tracks of repeating guanine units can form a number of quadruplexes that are distinguished by their strand number, strand orientation, and loop types. The structural topologies of DNA quadruplexes also drastically change with slight changes of the DNA sequences, with the nature of the cationic species and with their concentrations in solution. As a result, the structures of DNA quadruplexes are far from being fully recognized and have been of concern to researchers because of their potential implications in biological and structural applications.Development in electrospray ionization mass spectrometry (ESI-MS) has been shown to be superior in the analysis of DNA noncovalent complexes in terms of speed, sensitivity, stoichiometry, and specificity compared to other analytical techniques [12]. Previous work by ourselves and others have shown that some specific DNA conformations, such as hairpins, triplexes, and quadruplexes formed in solution, can survive in the gas phase [13][14][15][16][17][18][19][20]. This prompted us to explore the structural properties of DNA quadruplexes with ESI-MS so as to add new information concerning them.

Formation and Dissociation of the Interstrand i-Motif by the Sequences d(XnC4Ym) Monitored with Electrospray Ionization Mass Spectrometry

“…Stock solutions of the oligomers were prepared by directly dissolving the lyophilized powder in Milli-Q water to approximate 2mM and were stored at -18°C. The exact concentration of the oligonucleotides was determined spectrophotometrically by measuring the absorbance at 260nm at elevated temperature (90°C) (http://scitools.idtdna.com/country.aspx) as described earlier [36].…”

“…5-ions [3,36], as shown in Figure S1 in Supporting Information. The source conditions were as follows: capillary 3300V, end plate offset -500V, dry heater 180°C, and nebulizer pressure 0.4bar.…”

“…It has been demonstrated that electrospray ionization mass spectrometry (ESI-MS) is well suited for stoichiometric determination of noncovalent interacting oligonucleotides, including DNA duplexes, triplexes, and G-quadruplexes [33][34][35]. We previously used ESI-MS to show that d(G 3 T 4 G 3 ) and d(G 4 T 4 G 3 ) form bimolecular quadruplexes in solution, that these gas-phase complexes associated with the same number of NH 4 + ions as had been seen in solution by NMR, and that high salt induced these bimolecular structures to form higher order complexes [36]. Recently, the i-motif has also been studied by ESI-MS, Rosu et al [37] detected an IR absorbance signature indicative of a C•C + base pair in gas-phase i-motif ions.…”

Evaluation of effects of bivalent cations on the formation of purine-rich triple-helix DNA by ESI-FT-MS

“…There are two possible structures, homoduplex and quadruplex, for this homodimer, since (GGA)n and (GGT)n were found to form either homoduplex or quadruplex in the solution [24,25]. The G-quadruplex shows a tendency to embed NH 4 ϩ between two Gquartets, to stabilize its structure, and yields NH 4 ϩ adducts of G-quartets in the ESI-MS spectra [15,16]…”

“…ESI-MS has been used for studies of noncovalent oligonucleotide complexes, including detection of complex structures of oligonucleotides in the gas phase, such as DNA hairpins, duplexes, triplexes, and quadruplexes [12][13][14][15][16][17]. Besides extensive studies of interactions between various DNA and drugs and proteins, the interactions of metals with nucleobases and oligonucleotides have been investigated [17][18][19][20][21].…”