A Conformationally Constrained Nucleotide Analogue Controls the Folding Topology of a DNA G-Quadruplex

Abstract

Guanine-rich DNA and RNA sequences can fold into unique structures known as G-quadruplexes. The structures of G-quadruplexes can be divided into several classes, depending on the parallel or antiparallel nature of the strands and the number of G-rich tracts present in an oligonucleotide. Oligonucleotides with single tracts of guanines form intermolecular parallel tetrameric G-quadruplexes. Oligonucleotides with two tracts of guanosines separated by two or more bases can form both intermolecular antiparallel fold-back dimeric and parallel tetrameric G-quadruplexes, and those with four tracts of guanosines can form both intramolecular parallel and antiparallel structures. Intramolecular G-qaudruplexes can fold into several folding topologies including antiparallel crossover basket, antiparallel chair, and parallel propeller. The ability to control the folding of G-quadruplexes would allow the physical, biochemical, and biological properties of these various folding topologies to be studied. Previously, the known methods to control the folding topology of G-quadruplexes included changing the buffer by varying the mono- and divalent cations that are present, and by changing the DNA sequence. Because the glycosidic bonds in the G-quartets of G-quadruplexes with parallel strands are in the anti conformation, we reasoned that incorporation of nucleoside analogues that prefer the anti conformation of the glycosidic bond into G-rich sequences would increase the preference for parallel G-quadruplex formation. As predicted, by positioning the conformationally constrained nucleotide analogue 2'-O-4'-C-methylene-linked ribonucleotide into specific positions of a DNA G-quadruplex we were able to shift the thermodynamically favored structure of a G-quadruplex from an antiparallel to a parallel structure.

Selection of G‐Quadruplex Folding Topology with LNA‐Modified Human Telomeric Sequences in K+ Solution

“…[29,32,33] We therefore extended our studies with dimeric LNA-modified G-quadruplexes based on the human telomeric sequence and designed three LNA oligonucleotides to modulate the equilibrium between parallel and antiparallel topologies. LNA2 formed a mixture of parallel and antiparallel G-quadruplexes, even though at 25 8C the ratio was 7:1 in favour of the parallel topology.…”

“…[30,31] In other cases, LNA incorporations in antiparallel fold-back G-quadruplex structures have led to decreases in thermostability, as observed for the unimolecular version of the O. nova G-quadruplex and the thrombin-binding quadruplex aptamer. [29,33] Thus, it appears that LNA modifications are better accommodated in the context of parallel quadruplex folding topologies, as gauged, for example, by the increase in thermostability of such Gquadruplexes and by the ability of LNA nucleotides to partake in native parallel DNA folds.…”

“…For example, the unimolecular O. nova sequence, which usually adopts an antiparallel fold, was modified by single LNA substitutions at various positions and, depending on the exact LNA position, a change in structure to a parallel topology was observed in some cases, while mixtures or unaltered topologies were observed in other cases in K + solution. [29] In the case of the dimeric O. nova sequence, when we replaced the four DNA-G residues located in anti positions with LNA-Gs, the folding topology changed completely to a striking and remarkable topology in which each Gtract followed a V-like trajectory. [32] We report herein a study of LNA-modified DNA sequences based on the two-repeat human telomere sequence in K + solutions using UV spectrophotometry and CD and NMR spectroscopies.…”

“…Some reports on LNA-modified G-quadruplexes have appeared, in which LNA was incorporated into unimolecular, dimeric, and tetrameric model systems based on the Oxytricha nova telomeric sequence, [29][30][31][32] or incorporated into the thrombin-binding aptamer. [33,34] In general, LNA-modified quadruplexes tend to favour parallel-stranded topologies, but a straightforward correlation between LNA substitution patterns and folding topology has not been established.…”

Chiralitätsverstärkung in dynamischen supramolekularen Aggregaten

“…Hierbei wurden konformative Effekte genutzt, um Strukturänderungen in Polymeren herbeizufüh-ren: [115,116] [123] Foldamere sind eine interessante Klasse von Oligomeren/ Polymeren. Sie verhalten sich in Lösung gewöhnlich wie Polymere mit Zufallsstruktur, aber unter bestimmten Bedingungen können sie bevorzugt eine helikale Orientierung einnehmen und sich in diesem Zustand zu kolumnaren Strukturen stapeln.…”