Specific loop modifications of the thrombin‐binding aptamer trigger the formation of parallel structures

Abstract

Guanine-rich sequences show large structural variability, with folds ranging from duplex to triplex and quadruplex helices. Quadruplexes are polymorphic, and can show multiple stoichiometries, parallel and antiparallel strand alignments, and different topological arrangements. We analyze here the equilibrium between intramolecular antiparallel and intermolecular parallel G-quadruplexes in the thrombin-binding aptamer (TBA) sequence. Our theoretical and experimental studies demonstrate that an apparently simple modification at the loops of TBA induces a large change in the monomeric antiparallel structure of TBA to yield a parallel G-quadruplex showing a novel T-tetrad. The present results illustrate the extreme polymorphism of G-quadruplexes and the ease with which their conformation in solution can be manipulated by nucleotide modification.Abbreviations

Spectroscopic Properties of Two 5′-(4-Dimethylamino)Azobenzene Conjugated G-Quadruplex Forming Oligonucleotides

“…These data indicated that the presence of the dye induced the shift of the TBA folding from a monomolecular- to multimeric- Q. In line with these results, previously reported studies have demonstrated the sensitivity of the TBA-Q typology to such specific modifications [ 62 ]. In order to obtain additional information about the structural features of the 5′-DMAzo-TBA-Qs fluorescence experiments were also performed irradiating at 255 nm the 5′-DMAzo-TBA or TBA in both the 100 K buffer and 5KEW.…”

Clustered abasic lesions profoundly change the structure and stability of human telomeric G-quadruplexes

“…Less is known about clusters of natural lesions in non-canonical, unusual DNA and RNA structures, such as the G-quadruplex which is currently the most comprehensively studied non-B model (18). Regarding G-quadruplex modifications that can be defined retroactively as clustered modifications, multiple mutations by natural and synthetic bases of the guanines in the G-tetrads as well as of the bases in loops should be mentioned (19–24). In this study, we only deal with clustered natural lesions in quadruplexes.…”

Unusual Chair-Like G-Quadruplex Structures: Heterochiral TBA Analogues Containing Inversion of Polarity Sites

“…Gel Electrophoresis. Since some authors have shown that site-specific changes in the TBA sequence can result in the formation of bimolecular structures [17], before further investigations, ODNs H1, H2, and H3 have been analyzed by PAGE, in which the TBA has been used as a reference (Figure 2). As it is evident from the electropherogram, all the three investigated heterochiral ODNs show a main band with electrophoretic motilities very similar to TBA, thus strongly suggesting the occurrence of major monomolecular G-quadruplex structures resembling the TBA chair-like Gquadruplex.…”