摘要
We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.
We study the properties of the ethylene glycol solutions and the conformational transitions of DNA segment in the ethylene glycol solutions by molecular dynamics simulations based on GROMACS. The hydrogen network structures of water–water and ethylene glycol–water are reinforced by ethylene glycol molecules when the concentrations of the solutions increase from 0% to 80%. As illustrated by the results, conformation of the double-stranded DNA in ethylene glycol solutions, although more compact, is similar to the structure of DNA in the aqueous solutions. In contrast, the DNA structure is an A–B hybrid state in the ethanol/water mixed solution. A fraying of terminal base-pairs is observed for the terminal cytosine. The ethylene glycol molecules preferentially form a ring structure around the phosphate groups to influence DNA conformation by hydrogen interactions, while water molecules tend to reside in the grooves. The repulsion between the negatively charged phosphate groups is screened by ethylene glycol molecules, preventing the repulsion from unwinding and extending the helix and thus making the conformation of DNA more compact.
作者
张楠
李明儒
张丰收
Nan Zhang1, Ming-Ru Li2, and Feng-Shou Zhang1,2,3(1 Key Laboratory of Beam Technology of Ministry of Education, College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875, China 2Beijing Radiation Center, Beijing 100875, China 3 Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator ofLanzhou, Lanzhou 730000, China)
基金
Project supported by the National Natural Science Foundation of China(Grant Nos.11635003,11025524,and 11161130520)
the National Basic Research Program of China(Grant No.2010CB832903)
the European Commissions 7th Framework Programme(FP7-PEOPLE-2010-IRSES)(Grant No.269131)
