Structural varieties of selectively mixed G- and C-rich short DNA sequences studied with electrospray ionization mass spectrometry

Abstract

Short guanine(G)-repeat and cytosine(C)-repeat DNA strands can self-assemble to form four-stranded G-quadruplexes and i-motifs, respectively. Herein, G-rich and C-rich strands with non-G or non-C terminal bases and different lengths of G- or C-repeats are mixed selectively in pH 4.5 and 6.7 ammonium acetate buffer solutions and studied by electrospray ionization mass spectrometry (ESI-MS). Various strand associations corresponding to bi-, tri- and tetramolecular ions are observed in mass spectra, indicating that the formation of quadruplex structures is a random strand by strand association process. However, with increasing incubation time for the mixtures, initially associated hybrid tetramers will transform into self-assembled conformations, which is mainly driven by the structural stability. The melting temperature values of self-assembled quadruplexes suggest that the length of G-repeats or C-repeats shows more significant effect on the stability of quadruplex structures than that of terminal residues. Accordingly, we can obtain the self-associated tetrameric species generated from the mixtures of various homologous G- or C-strands efficiently by altering the length of G- or C-repeats. Our studies demonstrate that ESI-MS is a very direct, fast and sensitive tool to provide significant information on DNA strand associations and stoichiometric transitions, particularly for complex mixtures. Copyright © 2016 John Wiley & Sons, Ltd.

Investigation and improvement of catalytic activity of G-quadruplex/hemin DNAzymes using designed terminal G-tetrads with deoxyadenosine caps

“…30,49 These observations are also in line with previous reports, which have shown that the species of short anking residues have a low effect on the G-tetrad stacking modes of four-stranded G4s. [50][51][52] Similar results were also observed for the strands annealed in KCl buffer at pH 7.4 ( Fig. S1B, ESI †).…”

Construction of a junction DNA nanostructure and modulation of the junction switching to quadruplexes

“…However, this may also induce the formation of interlocked duplex DNA structures, which results in low structural conversion efficiency from the ‘duplex + quadruplex’-type DNA nanostructures to the junction DNA nanostructures. Our previous results have revealed that G- or C-rich strands can undergo ‘self-assembly’ in the formation of quadruplex structures by altering the length of the G- or C-repeats [ 31 ]. Following on from this work, we will optimize the nature of the G- and C-rich strands to improve the operation mechanism of the potential ‘DNA nanomachine’.…”

5′-(CGA) n sequence-assisted pH-controlled assembly of supramolecular DNA nanostructure

“…By using ESI-MS, we can obtain accurate information on association preference of G-rich and C-rich DNA strands in various solution conditions [26] and have built a novel DNA nanostructure with both G-quadruplex and i-motif based on ESI-MS determinations [21]. In this work, we attempted to construct G-quadruplex-based supramolecular nanostructures and regulate the assembly of the nanostructures by connecting a specific 5′-(CGA) n sequence which can form pH-dependent DNA duplex.…”

“…Following that, we used the sequence d(G 6 ) to link S1 and CS1, S2 and CS2, which formed the sequences d(CGACGAG 6 AGCAGC) (SG1) and d(GCTGCTG 6 TCGTCG) (CSG1), respectively; and used d(T 2 G 6 T 2 ) to link S1 and S2, CS1 and CS2 which formed the sequences d(CGACGATTG 6 TTAGCAGC) (SG2) and d(GCTGCTTTG 6 TTTCGTCG) (CSG2), respectively (table 1). Thus, the strands SG1, SG2, CSG1 and CSG2 containing consecutive six Gs in the centre were supposed to form stable parallel tetramolecular G-quadruplex core in KOAc buffer solution (structures A–C in figure 2; electronic supplementary material, figure S1 a – f ) [26]. Specifically, SG2 could form a G-quadruplex dimer (A in figure 2) connected by II-DNA structure of 5′-(CGA) n sequences at pH 4.5, and a mixture of SG2 and CSG2 (at a molar ration of 1 : 1) could generate a G-quadruplex tetramer in acidic solution (D in figure 2).…”

“…Previously, we have demonstrated that electrospray ionization mass spectrometry (ESI-MS) is a powerful tool for monitoring stoichiometry of DNA complexes associated by various strands [3,21,22,26] because soft ionization technique of ESI is able to maintain non-covalent interactions of inter-molecules during their transfer from solution to the gas phase. By using ESI-MS, we can obtain accurate information on association preference of G-rich and C-rich DNA strands in various solution conditions [26] and have built a novel DNA nanostructure with both G-quadruplex and i-motif based on ESI-MS determinations [21]. In this work, we attempted to construct G-quadruplex-based supramolecular nanostructures and regulate the assembly of the nanostructures by connecting a specific 5 -(CGA) n sequence which can form pH-dependent DNA duplex.…”