Recent progress in atomistic simulation of electrical current DNA sequencing

Abstract

We review recent advances in the DNA sequencing based on the measurement of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices.

Optical fingerprints and electron transport properties of DNA bases adsorbed on monolayer MoS2

“…Particularly, MoS 2 -based TMDs monolayers, due to its exotic electronic and transport properties, remain a testing ground for sensing applications 19,21,22 e.g. the photoluminescence spectra (PL) of MoS 2 reveals the possibility of optical biosensors 19 ; modulation in PL due to the presence of DNA base could serve as a fingerprint for selective optical biosensing 19 ; nano-pore in pristine MoS 2 results in fast detection of DNA bases 17 ; MoS 2 based biomedical sensor shows promise to detect DNA origami, tumor necrosis factor-alpha (TNF-a) molecules etc.…”

Theoretical assessment of feasibility to sequence DNA through interlayer electronic tunneling transport at aligned nanopores in bilayer graphene

“…In search of new possibilities, the use of nanopore technologies has gained momentum 5 . The general idea is to drive the DNA molecule through a tiny hole in a biological 6 7 8 or solid-state 9 10 11 membrane while measuring the ionic current in the solution 12 13 or the transverse current 14 15 being conducted in the membrane itself. The first approach utilizes the fact that the magnitudes of ionic current blockage vary significantly when different types of nucleotides pass through the biological nanopore 6 7 8 12 13 .…”

Modeling of Ion and Water Transport in the Biological Nanopore ClyA

“…The transport of ions and molecules through nanoscale geometries is a field of intense study that uses both experimental, theoretical and computational methods. [1][2][3][4][5][6] One of the primary driving forces behind this research is the development of nanopores as label-free, stochastic sensors at the ultimate analytical limit (i.e., single molecule). 7-10 Such detectors have applications ranging from the analysis of biopolymers such as DNA [11][12][13][14][15][16][17][18] or proteins, [19][20][21][22][23] to the detection and quantification of biomarkers, [24][25][26][27][28][29][30] to the fundamental study of chemical or enzymatic reactions at the single molecular level.…”