Hydration Is a Major Determinant of the G-Quadruplex Stability and Conformation of the Human Telomere 3′ Sequence of d(AG₃(TTAG₃)₃)

Abstract

The factors that determine the conformation and stability of G-quadruplex forming sequences remain poorly understood. Here we demonstrate the influence of cosolvents on the conformation and stability of the human telomeric sequence d(A(GGGTTA)3GGG)) in both K(+) and Na(+) containing solutions using a combination of circular dichroism, NMR, and thermodynamics. Molecular crowding arguments have previously been used to suggest that the parallel quadruplex form may be biologically relevant. However, the small cosolvents previously used, PEG 200 and 400, are actually dehydrating agents. We have used acetonitrile as a non-hydrogen-bonding dehydrating agent; similar conformational transitions were observed in K(+) solution. Moreover, NMR analysis shows that the resulting structure contains non-anti guanine glycosyl torsion angles suggesting that the conformation present in acetonitrile is not identical to the all-parallel crystal structure, despite the supposed parallel type CD spectrum.

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].…”

Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity

“…The loop topology of the hybrid fold consists of a double-chain reversal loop and two edgewise loops, in which hybrid-1 and hybrid-2 differ only in the location of the double-chain reversal, 5′ vs. 3′. In contrast to the hybrid folds, the propeller fold is observed in KCl solutions bearing high concentrations of organic solvents and consists of a parallel strand arrangement, with all G nucleotides adopting the anti conformation; all three loops are double-chain reversals (1,9,10). More recently, the propeller fold also was observed under conditions of high viscosity (11).…”

Diverse effects of naturally occurring base lesions on the structure and stability of the human telomere DNA quadruplex

“…Ethyl alcohol [25,58,59], like many other small molecular cosolvents, such as glycerol, ethylene glycol [60], acetonitrile [61] and also macromolecular crowding simulating agents, such as PEG of various lengths [62e64] can convert the antiparallel and hybrid quadruplexes into parallel forms. The adenine AP site in any loop of the 22mer quadruplexes largely facilitated this transition by ethanol, compared to the wt quadruplex (Fig.…”