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

• Published in: Methods (San Diego, Calif.) Vol. 57; no. 1; pp. 76 - 83
• Main Authors: Petraccone, Luigi, Pagano, Bruno, Giancola, Concetta
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2012
• Subjects: Circular Dichroism; Crowding; Dehydration; DNA; DNA - chemistry; fluorescence; G-quadruplex; G-Quadruplexes; Guanine - chemistry; Hydration; isomerization; Kinetics; Ligands; Molecular crowding; Nucleic Acid Conformation; Oligonucleotides - chemistry; proteins; solutes; Solutions; Spectroscopic methodologies; spectroscopy; Telomere; Thermodynamics; Water - chemistry; Water activity; Spectroscopic methodologies; Molecular crowding; Hydration; G-quadruplex
• ISSN: 1046-2023; 1095-9130; 1095-9130
• DOI: 10.1016/j.ymeth.2012.02.011

[Display omitted] ► Methods to study the effects of crowding/dehydrating agents on DNA G-quadruplexes. ► Effect of crowding/dehydrating agents on quadruplex stability. ► Effect of crowding/dehydrating agents on quadruplex–duplex equilibria. ► Effect of crowding/dehydrating agents on G-quadruplex binding properties. Intracellular environment is crowded with biomolecules that occupy a significant fraction (up to 40%) of the cellular volume, with a total concentration in the range 300–400mg/ml. Recently, the effect of crowding/dehydrating agents on the DNA G-quadruplexes has become a subject of an increasing interest. Crowding and/or dehydrating agents have been used to simulate how G-quadruplexes behave under cell-mimicking conditions characterized by a large excluded volume and a lower water activity. Indeed, the presence of both steric crowding and a lower water activity can affect G-quadruplex stability, their folding/unfolding kinetics, as well as their binding processes with proteins or small ligands. Many of these effects can be explored experimentally by measuring the dependence of the conformational stability, isomerisation kinetics and equilibria on the concentration of cosolutes which do not interact with the molecules (G-quadruplexes) under investigation. Spectroscopic methodologies, like circular dichroism, UV and fluorescence, have been widely employed to study G-quadruplexes in dilute solution. Here we focus on some aspects that need to be taken into account when employing such techniques in the presence of large amount of a cosolute. Additionally, we discuss possible problems/artifacts that arise in setting experiments in presence of these commonly employed cosolutes and in interpreting the results.