Nanopore

A nanopore is a small hole in an electrically insulating membrane, that can be used as a single-molecule detector. It may be considered a Coulter counter for much smaller particles. It can be a biological protein channel in a high electrical resistance lipid bilayer, a pore in a solid-state membrane or a protein channel set in a synthetic membrane. The detection principle is based on monitoring the ionic current passing through the nanopore as a voltage is applied across the membrane. When the nanopore is of molecular dimensions, passage of molecules (e.g., DNA) cause interruptions of the "open" current level, leading to a "translocation event" signal. The passage of RNA or single-stranded DNA molecules through the membrane-embedded alpha-hemolysin channel (1.5 nm diameter), for example, causes a ~90% blockage of the current (measured at 1 M KCl solution).^[1]

Solid State Nanopores

Solid-state nanopores are generally made in silicon compound membranes, one of the most common being silicon nitride. Solid-state nanopores can be manufactured with several techniques including ion-beam sculpting^[2] and electron beams.^[3]

Nanopores may also be used to identify analytes other than DNA. Professor Hagan Bayley’s Research team at the University of Oxford has published research that uses protein nanopores to differentiate between enantiomers of small molecules such as ibuprofen and thalidomide,^[4] identify specific biomarkers^[5] and screen ion channels.^[6] These might have broader applications in clinical medicine and drug development.

Nanopore Based Sequencing

The observation that a passing strand of RNA containing different bases results in different blocking levels has led to the nanopore sequencing hypothesis. Oxford Nanopore Technologies and Professor Hagan Bayley's laboratories have shown identification of individual nucleotides including methylated cytosine as they pass through a modified hemolysin nanopore.^[7]

Such sequencing, if successful, could revolutionize the field of genomics, as sequencing would be simplified and have the potential for dramatic improvements in power and cost over current versions that use fluorescence/luminescence and optical instrumentation to detect this photon signal. Apart from rapid DNA sequencing, other applications include separation of single stranded and double stranded DNA in solution, and the determination of length of polymers. At this stage, nanopores are making contributions to the understanding of polymer biophysics, as well as to single-molecule analysis of DNA-protein interactions.

Size Tunable Nanopores

Size-tunable elastomeric nanopores have been fabricated, allowing accurate measurement of nanoparticles as they occlude the flow of ionic current.This measurement methodology can be used to measure a wide range of particle types. In contrast to the limitations of solid-state pores, they allow for the optimisation of the resistance pulse magnitude relative to the background current by matching the pore-size closely to the particle-size. As detection occurs on a particle by particle basis, the true average and polydispersity distribution can be determined.^[8][9] Using this principle, the world's only commercial tunable nanopore-based particle detection system has been developed by Izon Science Ltd.

Alternate Definition

These can be about 20 nm in a diameter. They are integrated into artificially constructed encapsulated cells of silicon wafers. These pores allow small molecules like oxygen, glucose and insulin to pass however they prevent large immune system molecules like immunoglobins from passing. This way rat pancreatic cells are microencapsulated, they receive nutrients and release insulin through nanopores being totally isolated from their neighboring environment i.e foreign cells. This knowledge can help to replace nonfunctional islets of Langerhans cells in the pancreas (responsible for producing insulin), by harvested piglet cells. They can be implanted underneath the human skin without the need of immunosuppressants which put diabetic patients at a risk of infection.

Research News

Inspired by the biological ion channel, a synthetic film with a single nanopore structure was prepared as described by Apel et al. Unlike the fragile lipid-bilayer membrane in which most natural ion channels are embedded, this synthetic film is mechanically and chemically robust. Even though ion channels in living organisms have been studied by a mimic method using synthetic nanopores during the past several decades, how to endow these synthetic nanopores with intelligence is still a challenging task. Prof. Lei Jiang and his colleagues extend the function of molecule — nanopore systems by using G-quadruplex DNA. In their biomimetic nanochannel system, there is an ion concentration effect, which is a very important phenomenon in a living body and other systems do not have. Their novel biomimetic nanochannel system was responsive to potassium ion within a certain concentration range and simulated these processes in a pH-neutral environment as in a natural organism. In their work, the situation of the grafting G-quadruplex DNA on a single nanopore can closely imitate the in vivo condition because the G-rich telomere overhang is attached to the chromosome. Therefore, their artificial system could promote a potential to conveniently study biomolecule conformational change in confined space by the current measurement, which is significantly different from the nanopore sequencing. Moreover, such a system may also potentially spark further experimental and theoretical efforts to simulate the process of ion transport in living organisms and can be further generalized to other more complicated functional molecules for the exploitation of novel bioinspired intelligent nanopore machines.

See also

• Nanopore sequencing
• Nanofluidics

References

1. ^ Akeson M, Branton D, Kasianowicz JJ, Brandin E, Deamer DW (December 1999). "Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules". Biophys. J. 77 (6): 3227–33. doi:10.1016/S0006-3495(99)77153-5. PMC 1300593. PMID 10585944. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1300593. 
2. ^ Li J, Stein D, McMullan C, Branton D, Aziz MJ, Golovchenko JA (July 2001). "Ion-beam sculpting at nanometre length scales". Nature 412 (6843): 166–9. doi:10.1038/35084037. PMID 11449268. 
3. ^ Storm AJ, Chen JH, Ling XS, Zandbergen HW, Dekker C (August 2003). "Fabrication of solid-state nanopores with single-nanometre precision". Nat Mater 2 (8): 537–40. doi:10.1038/nmat941. PMID 12858166. 
4. ^ Kang, XF; Cheley, S; Guan, X; Bayley, H (August 2006). "Stochastic detection of enantiomers". J Am Chem Soc 128 (33): 10684–5. doi:10.1021/ja063485l. PMID 16910655. 
5. ^ Cheley, S; Xie, H; Bayley, H (December 2006). "A genetically encoded pore for the stochastic detection of a protein kinase". Chembiochem 7 (12): 1923–7. doi:10.1002/cbic.200600274. PMID 17068836. 
6. ^ Syeda, R; Holden, MA; Hwang, WL; Bayley, H (2008). "Screening blockers against a potassium channel with a droplet interface bilayer array". J. Am. Chem. Soc. 130 (46): 15543–8. doi:10.1021/ja804968g. PMID 18950170. 
7. ^ Clarke J, Wu HC, Jayasinghe L, Patel A, Reid A, Bayley H (2009). "Continuous base identification for single-molecule nanopore DNA sequencing". Nature Nanotechnology 4 (4): 265–270. doi:10.1038/nnano.2009.12. PMID 19350039. http://www.nature.com/nnano/journal/v4/n4/full/nnano.2009.12.html. 
8. ^ G. Seth Roberts, Darby Kozak, Will Anderson, Murray F. Broom, Robert Vogel and Matt Trau. Tunable Nano/Micropores for Particle Detection and Discrimination: Scanning Ion Occlusion Spectroscopy". Small (2010) - Volume 6, Issue 23, pages 2653–2658.
9. ^ Stephen J. Sowerby, Murray F. Broom, George B. Petersen. "Dynamically resizable nanometre-scale apertures for molecular sensing" Sensors and Actuators B: Chemical Volume 123, Issue 1 (2007), pages 325-330

• Xu Hou, Wei Guo, Lei Jiang (2011). "Biomimetic Smart Nanopores and Nanochannels". Chem. Soc. Rev. 40 (5): 2041–3052. doi:10.1039/c0cs00053a. http://pubs.rsc.org. 

• Xu Hou, Lei Jiang (2009). "Learning from Nature: Building Bio-Inspired Smart Nanochannels". ACS Nano 3 (11): 3339–42. doi:10.1021/nn901402b. PMID 19928930. http://pubs.acs.org/doi/abs/10.1021/nn901402b. 

External links and references

• Links to nanopore research groups
• The Harvard Nanopore Group
• NanoSEQ — The Global Exchange for Nanopore Research
• Oxford Nanopore Technologies
• Nabsys
• Sequenom
• UC Santa Cruz Nanopore Project
• Wang H, Dunning JE, Huang AP, Nyamwanda JA, Branton D (September 2004). "DNA heterogeneity and phosphorylation unveiled by single-molecule electrophoresis". Proc. Natl. Acad. Sci. U.S.A. 101 (37): 13472–7. doi:10.1073/pnas.0405568101. PMC 518781. PMID 15342914. http://www.pnas.org/cgi/pmidlookup?view=long&pmid=15342914. 
• Computer simulations of nanopore devices
• Conical Nanopore Sensors
• Biomimetic Channels and Ionic Devices