An improved DNA force field for ssDNA interactions with gold nanoparticles
文献类型：期刊论文
| 作者 | Jiang, XK ; Gao, J ; Huynh, T ; Huai, P ; Fan, CH ; Zhou, RH ; Song, B |
| 刊名 | JOURNAL OF CHEMICAL PHYSICS
 |
| 出版日期 | 2014 |
| 卷号 | 140期号:23 |
| 关键词 | SINGLE-STRANDED-DNA COLORIMETRIC DETECTION MOLECULAR-MECHANICS SURFACE SCIENCE ADSORPTION SIMULATIONS NUCLEOBASES ENERGETICS SEQUENCES PROTEINS |
| ISSN号 | 0021-9606 |
| 通讯作者 | ruhongz@us.ibm.com ; bosong@sinap.ac.cn |
| 英文摘要 | The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices. (C) 2014 AIP Publishing LLC. |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000337886200005 |
| 公开日期 | 2015-03-13 |
| 源URL | [http://ir.sinap.ac.cn/handle/331007/14007]  |
| 专题 | 上海应用物理研究所_中科院上海应用物理研究所2011-2017年 |
| 推荐引用方式 GB/T 7714 | Jiang, XK,Gao, J,Huynh, T,et al. An improved DNA force field for ssDNA interactions with gold nanoparticles[J]. JOURNAL OF CHEMICAL PHYSICS,2014,140(23). |
| APA | Jiang, XK.,Gao, J.,Huynh, T.,Huai, P.,Fan, CH.,...&Song, B.(2014).An improved DNA force field for ssDNA interactions with gold nanoparticles.JOURNAL OF CHEMICAL PHYSICS,140(23). |
| MLA | Jiang, XK,et al."An improved DNA force field for ssDNA interactions with gold nanoparticles".JOURNAL OF CHEMICAL PHYSICS 140.23(2014). |
入库方式： OAI收割
来源：上海应用物理研究所
浏览0
下载0
收藏0
其他版本
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。