The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions

Abstract

G-quadruplex topologies of telomeric repeat sequences from vertebrates were investigated in the presence of molecular crowding (MC) mimetics, namely polyethylene glycol 200 (PEG), Ficoll 70 as well as Xenopus laevis egg extract by CD and NMR spectroscopy and native PAGE. Here, we show that the conformational behavior of the telomeric repeats in X. laevis egg extract or in Ficoll is notably different from that observed in the presence of PEG. While the behavior of the telomeric repeat in X. laevis egg extract or in Ficoll resembles results obtained under dilute conditions, PEG promotes the formation of high-order parallel topologies. Our data suggest that PEG should not be used as a MC mimetic.

Studying the effect of crowding and dehydration on DNA G-quadruplexes

“…Large amount of cosolutes have been used to simulate molecular crowding and/or dehydrating conditions in the attempt to clarify how G-quadruplexes behave under cell-mimicking conditions [10][11][12][13][14].…”

Long‐Range Distance Measurements on Nucleic Acids in Cells by Pulsed EPR Spectroscopy

“…[10] We recently demonstrated that DNA and RNA hairpins and DNA quadruplexes can be observed in Xenopus laevis oocytes by in-cell NMR spectroscopy. [11] In these experiments we showed that the conformation of a telomeric G-quadruplex sequence in vitro is different from that in a cellular environment. Here, we have used PELDOR spectroscopy on a double-labeled 12 base pair (bp) DNA duplex,…”

“…[15] The in-cell lifetimes of the tetraethyl-substituted pyrrolidine-and pyrroline-based nitroxide spin labels attached to NA molecules are expected to be even larger. In vitro PELDOR experiments were carried out in intraoocyte buffer [11] with a final concentration of 150 mm doublelabeled oligonucleotide. For the in-cell experiments, injection of 30-50 nL of 2.5-5 mm double-labeled NAs in roughly 50 oocytes takes up to 10 minutes (about 10 s for each oocyte, respectively).…”

Evaluating the Effects of the Nonplanarity of Nucleic Acid Bases on NMR, IR, and Vibrational Circular Dichroism Spectra: A Density Functional Theory Computational Study

“…The fact that the structures and dynamics of NAs are strongly sensitive to interactions with the surrounding environment, such as water molecules, ions, or molecular crowding, [1][2][3][4][5][6][7][8][9][10] makes NMR spectroscopy the exclusive tool for the structural characterization of NA under physiological conditions. 11 The glycosidic torsion angle ( torsion) is one of the fundamental local structural descriptors of NAs. The torsion measures the local orientation of an NA base with respect to the sugar ribose ( Figure 1).…”