All-atom steered molecular dynamics (SMD) simulations provide the means to study the single-stranded DNA (ssDNA) translocation through graphene nanopores at a controllable speed. The ssDNA is pulled by an elastic force similar to the manipulation by an AFM tip. At the same time, an electric field is applied across the reservoir along the direction of the pulling force, in order to hold the ssDNA strand taut and drive the ions in the solutions through the nanopore. By monitoring and analyzing the average ionic current blockage of poly(dA)10, poly(dC)10, poly(dG)10 and poly(dT)10, it is found that one can indeed discriminate the different DNA bases from each other by holding each nucleotide in the pore for sufficiently long time. It is obtained the average blocked ionic currents can be listed, in a increasing order, as IG<IA<IT, which is almost in agreement with the order of sizes of the four nucleotides (VG>VA>VT>VC), apart from C. The results indicate that physical occupancy of the nucleotide plays the major role in affecting average blocked ionic current when the DNA translocation speed is effectively slowed down. This work provides a clue for the further investigation to realize the discrimination of the four nucleotides by the method of actively controlling DNA molecule translocation speed through the nanopores.
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ASME 2015 International Mechanical Engineering Congress and Exposition
November 13–19, 2015
Houston, Texas, USA
Conference Sponsors:
- ASME
ISBN:
978-0-7918-5747-2
PROCEEDINGS PAPER
Molecular Dynamics Study of DNA Translocation Through Graphene Nanopores With Controllable Speed Available to Purchase
Jingjie Sha,
Jingjie Sha
Southeast University, Nanjing, China
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Yunfei Chen
Yunfei Chen
Southeast University, Nanjing, China
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Kun Li
Southeast University, Nanjing, China
Wei Si
Southeast University, Nanjing, China
Jingjie Sha
Southeast University, Nanjing, China
Yunfei Chen
Southeast University, Nanjing, China
Paper No:
IMECE2015-50858, V07BT09A005; 5 pages
Published Online:
March 7, 2016
Citation
Li, K, Si, W, Sha, J, & Chen, Y. "Molecular Dynamics Study of DNA Translocation Through Graphene Nanopores With Controllable Speed." Proceedings of the ASME 2015 International Mechanical Engineering Congress and Exposition. Volume 7B: Fluids Engineering Systems and Technologies. Houston, Texas, USA. November 13–19, 2015. V07BT09A005. ASME. https://doi.org/10.1115/IMECE2015-50858
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