Step-defect guided delivery of DNA to a graphene nanopore

Nature Nanotechnology
Manish Shankla, Aleksei Aksimentiev

Abstract

Precision placement and transport of biomolecules are critical to many single-molecule manipulation and detection methods. One such method is nanopore sequencing, in which the delivery of biomolecules towards a nanopore controls the method's throughput. Using all-atom molecular dynamics, here we show that the precision transport of biomolecules can be realized by utilizing ubiquitous features of graphene surface-step defects that separate multilayer domains. Subject to an external force, we found that adsorbed DNA moved much faster down a step defect than up, and even faster along the defect edge, regardless of whether the motion was produced by a mechanical force or a solvent flow. We utilized this direction dependency to demonstrate a mechanical analogue of an electric diode and a system for delivering DNA molecules to a nanopore. The defect-guided delivery principle can be used for the separation, concentration and storage of scarce biomolecular species, on-demand chemical reactions and nanopore sensing.

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Citations

Feb 20, 2020·Nanoscale·Yang LiuWeifeng Li
Aug 29, 2020·Nanoscale·Fábio A L de SouzaRodrigo G Amorim
Feb 2, 2021·Advanced Materials·Wayne YangCees Dekker
Feb 13, 2021·Trends in Biotechnology·Ioannis PrattisLuigi G Occhipinti
Mar 16, 2021·Advanced Science·David WinogradoffAleksei Aksimentiev
Jul 7, 2021·ACS Sensors·David J NiedzwieckiMarija Drndić
Jul 25, 2021·Small·Leonardo D MachadoDouglas S Galvão
Mar 21, 2020·ACS Nano·Jothi Priyanka ThiruramanMarija Drndić
Jan 8, 2021·The Journal of Physical Chemistry Letters·Changxiong HuangJun Fan

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Methods Mentioned

BETA
atomic force microscopy
AFM

Software Mentioned

SMD
3D
Gwyddion package
DART
NAMD2
Inorganic Builder
VMD
CHARMM27

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