In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density ...In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH2 group of G or A base is abstracted by the ·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH2 group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ·OH-radical in living cells.展开更多
[目的]利用本课题组发展的定量分析方法研究激发态DNA碱基对分子间相互作用的本质,以及不同类型的电子跃迁对DNA碱基对分子间相互作用的影响.[方法]采用广义Kohn-Sham能量分解分析方法(generalized Kohn-Sham based energy decompositio...[目的]利用本课题组发展的定量分析方法研究激发态DNA碱基对分子间相互作用的本质,以及不同类型的电子跃迁对DNA碱基对分子间相互作用的影响.[方法]采用广义Kohn-Sham能量分解分析方法(generalized Kohn-Sham based energy decomposition analysis,GKS-EDA),对两种Waston-Crick构型和两种stacked构型的DNA碱基对分子间相互作用本质进行理论研究.[结果]对于Waston-Crick构型的碱基对,n→π^(*)跃迁削弱了轨道极化作用但加强了电子相关作用,激发态分子间相互作用由电子相关作用主导,而π→π^(*)跃迁对分子间氢键影响较小;对于stacked构型的碱基对,π→π^(*)跃迁削弱了静电相互作用但增强了电子相关作用.[结论]Waston-Crick构型碱基对分子间相互作用本质受电子激发跃迁影响较大,而电子激发跃迁基本不改变stacked构型碱基对分子间相互作用本质.展开更多
Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices...Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.展开更多
文摘In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH2 group of G or A base is abstracted by the ·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH2 group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ·OH-radical in living cells.
文摘[目的]利用本课题组发展的定量分析方法研究激发态DNA碱基对分子间相互作用的本质,以及不同类型的电子跃迁对DNA碱基对分子间相互作用的影响.[方法]采用广义Kohn-Sham能量分解分析方法(generalized Kohn-Sham based energy decomposition analysis,GKS-EDA),对两种Waston-Crick构型和两种stacked构型的DNA碱基对分子间相互作用本质进行理论研究.[结果]对于Waston-Crick构型的碱基对,n→π^(*)跃迁削弱了轨道极化作用但加强了电子相关作用,激发态分子间相互作用由电子相关作用主导,而π→π^(*)跃迁对分子间氢键影响较小;对于stacked构型的碱基对,π→π^(*)跃迁削弱了静电相互作用但增强了电子相关作用.[结论]Waston-Crick构型碱基对分子间相互作用本质受电子激发跃迁影响较大,而电子激发跃迁基本不改变stacked构型碱基对分子间相互作用本质.
文摘Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.
