Processes of DNA condensation induced by multivalent cations： Approximate annealing experiments and molecular dynamics simulations |
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| Authors: | Chai Ai-Hua Ran Shi-Yong Zhang Dong Jiang Yang-Wei Yang Guang-Can and Zhang Lin-Xi |
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| Affiliation: | [1]Department of Physics, Zhejiang University, Hangzhou 310027, China [2]College of Mathematics, Physics and Information Engineering, Jiaxing University, Jiaxing 314001, China [3]Department of Physics, Wenzhou University, Wenzhou 325027, China |
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| Abstract: | The condensation of DNA induced by spermine is studied by atomic force microscopy (AFM) and molecular dynamics (MD) simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics (SMD) simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA-cation complexes. |
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| Keywords: | DNA condensation multivalent cations molecular dynamics simulation |
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