title: An improved DNA force field for ssDNA interactions with gold nanoparticles.
abstract: 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.
authors: Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800-204, Shanghai 201800, China.
authors: Xiankai
authors: X
authors: Jiang
authors: School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, People's Republic of China.
authors: Jun
authors: J
authors: Gao
authors: IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
authors: Tien
authors: T
authors: Huynh
authors: Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800-204, Shanghai 201800, China.
authors: Ping
authors: P
authors: Huai
authors: Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800-204, Shanghai 201800, China.
authors: Chunhai
authors: C
authors: Fan
authors: IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
authors: Ruhong
authors: R
authors: Zhou
authors: Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P. O. Box 800-204, Shanghai 201800, China.
authors: Bo
authors: B
authors: Song
mesh_terms: D000327:Adsorption; D004277:DNA, Single-Stranded / Q000737:chemistry*; D006046:Gold / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D053768:Metal Nanoparticles / Q000737:chemistry*; D056004:Molecular Dynamics Simulation
chemical_list: D004277:DNA, Single-Stranded; D006046:Gold