Solid-state and biological nanopore for real-time sensing of single chemical and sequencing of DNA

Abstract

Sensitivity and specificity are two most important factors to take into account for molecule sensing, chemical detection and disease diagnosis. A perfect sensitivity is to reach the level where a single molecule can be detected. An ideal specificity is to reach the level where the substance can be detected in the presence of many contaminants. The rapidly progressing nanopore technology is approaching this threshold. A wide assortment of biomotors and cellular pores in living organisms perform diverse biological functions. The elegant design of these transportation machineries has inspired the development of single molecule detection based on modulations of the individual current blockage events. The dynamic growth of nanotechnology and nanobiotechnology has stimulated rapid advances in the study of nanopore based instrumentation over the last decade, and inspired great interest in sensing of single molecules including ions, nucleotides, enantiomers, drugs, and polymers such as PEG, RNA, DNA, and polypeptides. This sensing technology has been extended to medical diagnostics and third generation high throughput DNA sequencing. This review covers current nanopore detection platforms including both biological pores and solid state counterparts. Several biological nanopores have been studied over the years, but this review will focus on the three best characterized systems including α-hemolysin and MspA, both containing a smaller channel for the detection of single-strand DNA, as well as bacteriophage phi29 DNA packaging motor connector that contains a larger channel for the passing of double stranded DNA. The advantage and disadvantage of each system are compared; their current and potential applications in nanomedicine, biotechnology, and nanotechnology are discussed.

Direct observation of DNA knots using a solid-state nanopore

“…Solid-state nanopores have emerged as an important tool with a large number of potential applications 22,23 at the crossroads of physics, biology and chemistry. Nanopores have provided a method to investigate various concepts in polymer physics such as polymer translocation through pores 24,25 , the Zimm relaxation time 25,26 , and the polymer capture process 27,28 .…”

A graphene field-effect transistor as a molecule-specific probe of DNA nucleobases

“…Electrical sequencing using graphene and nanopore technologies has recently attracted great attention due to the possibility to provide real-time sequencing of a whole single DNA molecule [3][4][5][6][7][8][9][10][11] . These methods are based on the use of graphene as an electrical readout-based chemical sensor while a strand of DNA is fed through a nanopore [2][3][4]10 . Most of the graphene-based sequencing technologies are fundamentally reliant on detecting molecular-specific interactions of individual nucleobases with a graphene surface 4 or its defects 5 .…”

Biological Nanomotors with a Revolution, Linear, or Rotation Motion Mechanism

“…The revolution mechanism offers a hint for the design of nanomolecular motors that can manipulate biomolecules in a controlled fashion. These nanomachines can also be applied for the construction of sophisticated nanodevices, including molecular sensors (221)(222)(223), bioreactors (224), chips (225), DNA-sequencing apparatuses (169,221,(226)(227)(228)(229), or other electronic and optical devices (230,231). In addition, these multisubunit biocomplexes could serve as drug targets for therapeutics and have potential for diagnostic applications (222,223,232,233), especially as the biomotors have an advantage of a high stoichiometry that could be applied to solve the drug resistance issue (234,235).…”