Stabilization of DNA Structures with Poly(ethylene sodium phosphate)
详细信息 查看全文
- 作者：Rui Moriyama ; Yasuhiko Iwasaki ; Daisuke Miyoshi
- 刊名：Journal of Physical Chemistry B
- 出版年：2015
- 出版时间：September 10, 2015
- 年：2015
- 卷：119
- 期：36
- 页码：11969-11977
- 全文大小：452K
- ISSN：1520-5207
文摘
The structure and stability of biomolecules under molecular crowding conditions are of interest because such information clarifies how biomolecules behave under cell-mimicking conditions. The anionic surfaces of chromatin, which is composed of DNA strands and histone complexes, are concentrated in cell nuclei and thus generate a polyanionic crowding environment. In this study, we designed and synthesized an anionic polymer, poly(ethylene sodium phosphate) (PEP路Na), which has a nucleic acid phosphate backbone and created a cell nucleus-like environment. The effects of molecular crowding with PEP路Na on the thermodynamics of DNA duplexes, triplexes, and G-quadruplexes were systematically studied. Thermodynamic analysis demonstrated that PEP路Na significantly stabilized the DNA structures; e.g., a free energy change at 25 掳C for duplex formation decreased from 鈭?.6 to 鈭?2.8 kcal/mol with 20 wt % PEP路Na. Thermodynamic parameters further indicated that the factors for the stabilization of the DNA structures were dependent on sodium ion concentration. At lower polymer concentrations, the stabilization was attributed to a shielding of the electrostatic repulsion between DNA strands by the sodium ions of PEP路Na. In contrast, at higher polymer concentrations, the DNA structures were entropically stabilized by volume exclusion, which could be enhanced by electrostatic repulsion between phosphate groups in DNA strands and in PEP路Na. Additionally, increasing PEP路Na concentration resulted in increasing enthalpy of the DNA duplex but decreasing enthalpy of DNA G-quadruplex, indicating that the polymers also promoted dehydration of the DNA strands. Thus, polyanionic crowding affects the thermodynamics of DNA structures via the sodium ions, volume exclusion, and hydration. The stabilization of DNA by the cell nucleus-like polyanionic crowding provides new information regarding DNA structures and allows for modeling reactions in cell nuclei.