CAS OpenIR  > 中科院上海应用物理研究所2011-2019年
An improved DNA force field for ssDNA interactions with gold nanoparticles
Jiang, XK; Gao, J; Huynh, T; Huai, P; Fan, CH; Zhou, RH; Song, B; ruhongz@us.ibm.com; bosong@sinap.ac.cn
2014
Source PublicationJOURNAL OF CHEMICAL PHYSICS
ISSN0021-9606
Volume140Issue:23
AbstractThe 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.
KeywordSingle-stranded-dna Colorimetric Detection Molecular-mechanics Surface Science Adsorption Simulations Nucleobases Energetics Sequences Proteins
Indexed BySCI
Language英语
WOS IDWOS:000337886200005
Citation statistics
Cited Times:9[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.sinap.ac.cn/handle/331007/14007
Collection中科院上海应用物理研究所2011-2019年
Corresponding Authorruhongz@us.ibm.com; bosong@sinap.ac.cn
Recommended Citation
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.,...&bosong@sinap.ac.cn.(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).
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