Effects of Graphene Nanopore Geometry on DNA Sequencing.
In this Letter we assess the effect of graphene nanopore geometries on DNA sequencing by considering DNA fragments including A, T, C, G, and 5-methylcytosine (MC) pulled out of graphene nanopores of different geometries with diameters down to ∼1 nm. Using steered molecular dynamics simulations it is demonstrated that the bases (A, T, C, G, and MC) can be indentified at single-base resolution through the characteristic peaks on the force profile in a circular graphene nanopore but not in nanopores with other asymmetric geometries. Our study suggests that the graphene nanopore surface should be modified as symmetrically as possible in order to sequence DNA by atomic force microscopy or optical tweezers.
†Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China.
Zhisen
Z
Zhang
‡School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China.
Jiawei
J
Shen
§College of Automation, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China.
Hongbo
H
Wang
†Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China.
Qi
Q
Wang
†Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China.
Junqiao
J
Zhang
†Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, People's Republic of China.|∥Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden.
Lijun
L
Liang
∥Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden.
Hans
H
Ågren
∥Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden.
Yaoquan
Y
Tu
DNA sequencing; geometry; graphene nanopores; molecular simulation; symmetry