ITP OpenIR  > 理论物理所科研产出  > SCI论文
Wu, SG; Feng, D; Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.; Wu, SG (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
Free Energy Calculation for Base Pair Dissociation in a DNA Duplex
发表期刊ACTA PHYSICO-CHIMICA SINICA
语种英语
关键词Potential Of Mean Force Hydrogen Bond Molecular Dynamics Simulation Umbrella Sampling
摘要DNA is the main genetic material for living organisms including many viruses. DNA duplex, coded with A=T and G=C base pairs, is well suited for biological information storage. The interactions between two bases in a base pair contribute to the stability of DNA duplex, and are further related to gene replication and transcription. In this study, we use all-atom Molecular dynamics (MD) simulations combined with Umbrella sampling (US) method to determine the free energy profiles and explore the molecular details for base pair dissociations. Four groups of DNA duplexes with different sequences have been constructed and a total of 4.3 mu s MD simulations have been carried out. In the potential of mean force (PMF) profile for G equivalent to C base pair dissociation (denoted as PMF-PGC), we observed three peaks, which correspond to the three moments G equivalent to C base pair loses its three hydrogen bonds respectively. Differently, A=T base pair loses its two hydrogen bonds within a very short time. As a result, only one hydrogen bond rupture peak was observed in its PMF curve (denoted as PMF-PAT). Compared with PMF-PAT, the overall free energy barrier in PMF-PGC is higher, which is due to the better stability of G equivalent to C than A=T. In the latter sections of both PMFs, free energies are still increasing, which is mainly resulted from the rigidity of DNA duplex backbone. We have also investigated the impact of neighboring base pairs on the stability of middle one. It is found that neighboring G equivalent to C base pairs increase the stability of A=T base pair while neighboring C equivalent to G base pairs reduce the stability of A=T base pair. Additionally, neighboring T=A base pairs have little influence on the stability of A=T base pair.
2016
卷号32期号:5页码:1282-1288
学科领域Chemistry
DOIhttp://dx.doi.org/10.3866/PKU.WHXB201602185
收录类别SCI
项目资助者National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; National Natural Science Foundation of China [11405113] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science and Technology Plan of Sichuan Province, China [2010JY0122] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02] ; Science Research Fund of Sichuan Normal University, China [10MSL02]
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/21649
专题理论物理所科研产出_SCI论文
通讯作者Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.; Wu, SG (reprint author), Chinese Acad Sci, Inst Theoret Phys, State Key Lab Theoret Phys, Beijing 100190, Peoples R China.
推荐引用方式
GB/T 7714
Wu, SG,Feng, D,Wu, SG ,et al. Free Energy Calculation for Base Pair Dissociation in a DNA Duplex[J]. ACTA PHYSICO-CHIMICA SINICA,2016,32(5):1282-1288.
APA Wu, SG,Feng, D,Wu, SG ,&Wu, SG .(2016).Free Energy Calculation for Base Pair Dissociation in a DNA Duplex.ACTA PHYSICO-CHIMICA SINICA,32(5),1282-1288.
MLA Wu, SG,et al."Free Energy Calculation for Base Pair Dissociation in a DNA Duplex".ACTA PHYSICO-CHIMICA SINICA 32.5(2016):1282-1288.
条目包含的文件
文件名称/大小 文献类型 版本类型 开放类型 使用许可
Free Energy Calculat(2354KB) 开放获取--请求全文
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[Wu, SG]的文章
[Feng, D]的文章
[Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.]的文章
百度学术
百度学术中相似的文章
[Wu, SG]的文章
[Feng, D]的文章
[Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.]的文章
必应学术
必应学术中相似的文章
[Wu, SG]的文章
[Feng, D]的文章
[Wu, SG (reprint author), Sichuan Normal Univ, Coll Chem & Mat Sci, Chengdu 610068, Peoples R China.]的文章
相关权益政策
暂无数据
收藏/分享
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。