How to study G-quadruplex structures

Abstract

All guanine-rich DNA and RNA molecules tend to fold into inter-and intra-molecular structures called G-quadruplexes. The core of a G-quadruplex is composed of at least two adjacent G-tetrads stabilized by monovalent cations. While it has been suggested that there could potentially be over 375 000 quadruplex forming sequences in the human genome alone, only a small number of three-dimensional G-quadruplex structures are known. More structural data are needed to explain their presence and function in vivo. We offer here a short review of experimental methods commonly used to determine G-quadruplex topologies.

Tuning the Polymorphism of the Anti-VEGF G-rich V7t1 Aptamer by Covalent Dimeric Constructs

“…The presence of a minimum at 295 nm associated with the maximum at 273 nm is diagnostic of a G4 structure [49]. However, this minimum was not very pronounced, as already observed for V7t1 analyzed under the same saline conditions [17], suggesting that probably not all the oligonucleotide is folded into a G4 and additional structures can be present in solution [49][50][51]. The minimum around 295 nm, in the case of A. bisV7t1T7 and bisV7t1HEG2, was negligible, indicative of a low amount of G4 in these samples, perhaps due to a not complete unfolding/refolding of the structure at 90 • C. Slight differences between the covalent V7t1 dimers and, in the case of the same aptamer, between its N.A.…”

“…Completely different was the behavior of the A. samples (Figure 3b). In the Na + -rich medium, both A. bisV7t1T7 and bisV7t1HEG2 displayed CD spectra [51,56,57] with two positive bands Aiming at verifying if some duplex structures were present in our samples, the UV thermal denaturation/renaturation experiments were registered also at 260 nm. In all cases (here reported for bisV7t1T7 as a representative example, Figure S10) a progressive absorbance increase and decrease were respectively found during the heating and cooling experiments, but no net sigmoidal behavior was observed.…”

“…and A. form at 2 µM concentration. Differential spectra-representing the spectral difference between the unfolded and the folded oligonucleotide-have peculiar patterns allowing identifying different nucleic acid secondary structures, and in particular G-quadruplexes [49][50][51].…”

“…CD spectroscopy is a primary tool for the characterization of G4 structures/topologies [51], also particularly useful in the study of dimeric sequences [52]. Typical antiparallel G4 structures show positive Cotton effects with bands centered at ca.…”

Spectral properties and thermal stability of AS1411 G-quadruplex

“…1A and B, intensity of CD spectra around 220 nm and 265 nm has increased upon increment of ion concentration, representing formation of parallel structure [33,34]. Moreover, there has been a blue shift from 220 nm to 210 nm, which could be indicative of quadruplex formation [36]. Upon formation of parallel structure and increase of signal intensity at 265 nm and, the hidden peak at 290 nm starts disappearing.…”