title: Thermodynamics of DNA structures under molecular crowding conditions with neutral and positive charged cosolutes.
abstract: The condition in a living cell is molecularly crowded with various biomolecules. Especially, in cell nucleus, there are high concentrations of histone proteins around DNA. Here, we analyzed quantitatively the effects of cosolutes inducing molecular crowding and histone-mimicking peptides on the thermodynamics of DNA structural formation via Watson Crick or Hoogsteen base pairs. The free energy changes for DNA structure formations with Hoogsteen and Watson-Crick base pairs decreased and increased when the concentration of poly(ethylene glycol) 200 was increased from 0 to 40 wt%, respectively. Moreover, it was observed that a histone-mimicking peptide, which is a part of the binding site of histone H3, stabilized DNA structures only with Hoogsteen base pairs. These results show that a cell nucleus mimicking condition such as a molecular crowding condition in the presence of histone proteins, stabilize DNA structures containing Hoogsteen base pairs and destabilize those with Watson-Crick base pairs, leading to structural polymorphism of various DNA sequences under molecular crowding conditions that mimic those found in cell nucleus.
authors.affiliation: Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Higashinada-ku, Kobe 658-8501, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Miyoshi
authors.forename: Kaori
authors.initials: K
authors.lastname: Nakamura
authors.forename: Sanjukta
authors.initials: S
authors.lastname: Muhuli
authors.forename: Hisae Tateishi
authors.initials: HT
authors.lastname: Karimata
authors.forename: Naoki
authors.initials: N
authors.lastname: Sugimoto
mesh_terms: D020029:Base Pairing; D002467:Cell Nucleus / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006657:Histones / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011092:Polyethylene Glycols / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D006657:Histones; D010455:Peptides; D011092:Polyethylene Glycols; D004247:DNA