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
DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect ...DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics （MD） simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d（CGCGAATTCGCG）2, coion Cl- and counterions Li＋, Na＋, K＋, Rb＋ and Cs~ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. In- creasing KCI concentration in solution hinders the A-DNA^B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K＋ 〈 Rb＋ 〈 Cs＋ 〈 Na＋ 〈 Li＋. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation （MMSA）. The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.展开更多
Four double-stranded DNA films with different chain lengths were prepared on 3-aminopropyltriethoxysilane(APS)-modified mica surfaces in the NaCl solution with concentration ranging from 0.001 to 0.1 M.By using an ato...Four double-stranded DNA films with different chain lengths were prepared on 3-aminopropyltriethoxysilane(APS)-modified mica surfaces in the NaCl solution with concentration ranging from 0.001 to 0.1 M.By using an atomic force microscope,the force-distance curves and friction behaviour of each DNA film were studied in the NaCl solution that was used in the sample preparation.When adsorbed on mica as films in salt solution,the conformation of DNA molecules would be a combination of loops and"train-like".As the chain length increased from 50 to 20000 bp,the extension rate of DNA film increased from 7.1to 11.5 in 0.001 mol/L NaCl solution,which suggested that the DNA molecule with long chain likely resulted in more extended conformation.In addition,under low normal load,low NaCl concentration could increase the friction of DNA film and the chain length revealed insignificant effect on the friction force of DNA film.Therefore,long chain DNA with low salt concentration is more conducive to the nanopore sequencing process,since extended conformation can make DNA molecules easier to reach into nanopore and the high friction can reduce the translocation speed.These results may benefit the development of the third-generation sequencing technique based on nanopore.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.
基金supported by the National Natural Science Foundation of China(21176132 and 20876083)Specialized Research Fund for the Doctoral Program of Higher Education(20100002110024)
文摘DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics （MD） simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d（CGCGAATTCGCG）2, coion Cl- and counterions Li＋, Na＋, K＋, Rb＋ and Cs~ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. In- creasing KCI concentration in solution hinders the A-DNA^B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K＋ 〈 Rb＋ 〈 Cs＋ 〈 Na＋ 〈 Li＋. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation （MMSA）. The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.
基金supported by the National Basic Research Program("973" Project)(Grant No.2011CB707604)the Natural Science Foundation of China(Grant Nos.91323103,51375409,21222401)
文摘Four double-stranded DNA films with different chain lengths were prepared on 3-aminopropyltriethoxysilane(APS)-modified mica surfaces in the NaCl solution with concentration ranging from 0.001 to 0.1 M.By using an atomic force microscope,the force-distance curves and friction behaviour of each DNA film were studied in the NaCl solution that was used in the sample preparation.When adsorbed on mica as films in salt solution,the conformation of DNA molecules would be a combination of loops and"train-like".As the chain length increased from 50 to 20000 bp,the extension rate of DNA film increased from 7.1to 11.5 in 0.001 mol/L NaCl solution,which suggested that the DNA molecule with long chain likely resulted in more extended conformation.In addition,under low normal load,low NaCl concentration could increase the friction of DNA film and the chain length revealed insignificant effect on the friction force of DNA film.Therefore,long chain DNA with low salt concentration is more conducive to the nanopore sequencing process,since extended conformation can make DNA molecules easier to reach into nanopore and the high friction can reduce the translocation speed.These results may benefit the development of the third-generation sequencing technique based on nanopore.
