Investigation of the nanoviscosity effect of a G-quadruplex and single-strand DNA using fluorescence correlation spectroscopy

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Guanine (G)-quadruplexes are of interest because of their presence in the telomere sequence and the oncogene promoter region. Their diffusion and change of structure, especially in high viscosity solutions, are important for understanding their dynamics. G-quadruplexes may have less effective viscosity (nanoviscosity) when they are smaller than the solvent molecules. In this paper, we report the difference in the diffusion dynamics of the G-rich DNA sequences of single-strand DNA (ssDNA) and the G-quadruplex in aqueous, sucrose, and polyethylene glycol (PEG) solutions. From experiments with aqueous and sucrose solutions, we confirm that a simple diffusion model according to the viscosity is appropriate. In the PEG experiments, the nanoviscosity effect is observed according to PEG's molecular weight. In the PEG 200 solution, both the ssDNA and the G-quadruplex possess macroviscosity. In the PEG 10 000 solution, the G-quadruplex possesses nanoviscosity and the ssDNA possesses macroviscosity, whereas, in the PEG 35 000 solution, both ssDNA and the G-quadruplex possess nanoviscosity. The experimental results are consistent with the theoretical predictions.
Publisher
AMER INST PHYSICS
Issue Date
2015-01
Language
English
Article Type
Article
Keywords

POLYACRYLAMIDE GEL ELECTROPHORESIS; MOLECULAR-DYNAMICS SIMULATIONS; SEMIDILUTE POLYMER-SOLUTIONS; TELOMERIC REPEAT; PROBE DIFFUSION; HYALURONIC ACID; LIGAND-BINDING; NUCLEIC-ACIDS; HUMAN GENOME; PARTICLES

Citation

JOURNAL OF CHEMICAL PHYSICS, v.142, no.2

ISSN
0021-9606
DOI
10.1063/1.4905113
URI
http://hdl.handle.net/10203/195323
Appears in Collection
PH-Journal Papers(저널논문)
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