title: Factors regulating thermodynamic stability of DNA structures under molecular crowding conditions.
abstract: The condition in a living cell is molecularly crowded with various biomolecules. The total concentration of the biomolecules inside Escherichia coli is in the range of 300-400 g/L. This is distinct from typical biomolecular concentrations of less than 1g/L, which is generally used for experiments in vitro. Here, we analyzed quantitatively the effects of molecular crowding on the thermodynamics of antiparallel G-quadruplex formation via Hoogsteen base pairs and of antiparallel hairpin-looped duplex (HP duplex) formation via Watson-Crick base pairs. The free energy changes for G-quadruplex and duplex formations decreased and increased when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt%, respectively. These results showed that the antiparallel G-quadruplex is stabilized under molecular crowding conditions but the HP duplex is destabilized.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Hisae
authors.initials: H
authors.lastname: Karimata
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry; D020029:Base Pairing; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry; D011092:Polyethylene Glycols / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D052157:Aptamers, Nucleotide; C081676:thrombin aptamer; D011092:Polyethylene Glycols; D006147:Guanine; D004247:DNA