Studying the adsorption of DNA nanostructures on graphene in the aqueous phase using molecular dynamic simulations

• Published in: Journal of molecular graphics & modelling 2017-06, Vol.74, p.16-23
• Main Authors: Sun, Jixue, Li, Yang, Lin, Jianping
• Format: Article
• Language: English
• Subjects: Adsorption; Binding Sites; DNA - chemistry; DNA nanostructure; Graphene; Graphite - chemistry; Molecular Dynamics Simulation; Nanostructures; Nucleic Acid Conformation; Solutions; Structural fluctuation; Thermodynamics
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2017.03.003

[Display omitted] •The single-stranded DNA could be easily adsorbed on the graphene.•DNA polymer could be adsorbed on the graphene by the flexible single-stranded DNA.•The adsorption could reduce the shape deformation of planar DNA polymers. DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene. The interaction analyses and energetic calculations show that π-π interactions between single-stranded DNA and graphene are necessary for adsorption of the DNA nanostructures. Overall, this work examined the interactions between DNA and graphene at a large spatial scale with the hope that it provides a new strategy to stabilize DNA nanostructures.