Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM...Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.展开更多
基金support from the National Natural Science Foundation of China (21176132)the Specialized Research Fund for the Doctoral Program of Higher Education (2010000211024)
文摘Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.
