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NANOPORE
PRESENTED BY: KAMYAR KHOSHNEVISAN
DR.BORDBAR
May 2, 2017
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What is a Nanopore?
Nanopores occur in nature, and in the biological
literature they are simply known as pores when they
are more than 1 nm or so in diameter, or channels
when they are narrower.
 A nanopore is simply a small hole, of the order of 1
nanometer
in
internal
diameter.
Certain
transmembrane cellular proteins act as nanopores,
and nanopores have also been made by etching a
somewhat larger hole (several tens of nanometers) in
a piece of silicon, and then gradually filling it in using
ion-beam sculpting methods which results in a much
smaller diameter hole: the nanopore.

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



Classification:
Natural
Unnatural
Organic
Inorganic

Consist of carbon, silicon,silicates and polymers for
aggregate material.

using zeolite in membrane
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
the natural channels that have been engineered as
nanopores, the most prominent have been porins,
proteins that control the permeability of the bacterial
outer membrane,and a–hemolysin (aHL), a poreforming toxin secreted by Staphylococcus aureus.
Work on both these systems has been aided by highresolution crystal structures.(figure)
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
Protein pores are engineered by using mutagenesis
and targeted chemical modification.The primary
interest lies in engineering the interior (lumen) of the
pores.

Mutagenesis can be used to introduce any of the
twenty natural amino acids, which provide a variety of
side chains of differing size, shape, polarity, and
reactivity.
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-seven subunits
-each subunit contributing with two βstrands
to form a 14-stranded β-barrel protein pore
-cis entrance is ~70 Åabove the bilayer
-total of ~100 Å-long lumen
-average ~20 Åin internal diameter
-the trans entrance is close to the bilayer
surface
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
What Can a Nanopore Do?
Ion channels open, conduct ions selectively, and
close”
The nanopores we are considering also
conduct ions, and even thoughthe diameters of the
pores are larger than the typical ion channel, they do
exhibit at least modest ion selectivity.

Natural pores, such as gap junctions,can gate (open
and close in response to a stimulus), but so far little
attention has been given to this issue with engineered
nanopores.(figure in next page)
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Basic properties of channels and pores. (a) Ion conduction; (b) ion
selectivity; (c) gating;(d) channel block.
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What are the Potential Applications of Nanopores?
 separations with various modified inorganic
nanopores.

The separations have been based on several
properties including molecular mass,charge,
hydrophobicity, and even stereochemistry.

similar separations might be carried out with
engineered protein nanopores.
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
Another area of application of protein nanopores is in
cell permeabilization. Because of its importance, the
utility
of
reversible
plasma
membrane
permeabilization in cell and tissue preservation has
received the most attention.

Example of this application: Loading mammalian cells
with trehalose by using aHL-H5 pores,which can be
blocked completely by Zn(II) ions(figure next page)
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
Here example of fabrication procedure for ultrathin
nanopore membranes, combining the techniques of
hot embossing for replication of nanopores and
photolithography for production of the thin
membranes.The embossing masters are fabricated by
electron beam lithography allowing customisation of
the design of the nanopore arrays.
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
In a first step, the origination of nanostructures is
carried out using electron beam lithography to
produce an embossing stamp. Here the design can
be tailored to the customers requirements.
For nanopore replication, the stamp consists of nanosized pillars,which are pressed into a polymer resist
that has been softened by applying heat. The final
steps of the fabrication process involve etch
processes for patterntransfer and photolithography
with micromachining to produce the final 260 nm thick
membrane.
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
The prototype nanopore membrane chip contains four
membranes, three of which have a 50 to 200 μm
structured area.
o
Each membrane contains pores of a different
diameter of 550, 330 and 140 nm, and centre-tocentre distances of 0.3 to 1 μm, 0.5 to 1 μm and 1 to
2 μm, respectively. The fourth membrane was left
unstructured as a control.
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Nanopore membrane chip (pore arrays 10μm).
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Application in industry:

Purification with Nano Pores

NanoPore Thermal Insulation

Nanopore Technology for Biomedical Applications
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Schematic of gas permeation in a pressure
gradient through a membrane represented by
a cylindrical pore of radius H, length L. The
hardcore diameter of the spherical gas
molecules is σ.
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A molecular model of translocation events
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Translocation of single
stranded DNA through a
nanopore in Si3N4.
Simulation conditions:
Electrical field of 1.3x109
V/m generates a voltage
bias of 21 V across the
membrane; 1.3±0.1 nm
diameter pore; 5.2 nm
thick membrane; single
stranded (dC)20, 1M
solution of KCl; 40125
atoms simulated; total
simulation time is 1.3 ns;
NvT ensemble.
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References :
1.C. R. Martin, P. Kohli, Nature Rev. DrugDisc. 2003, 2, 29–37.
2.G. E. Schulz, Biochim. Biophys. Acta 2002, 1565, 308–317.
3.K. S. Åkerfeldt, J. D. Lear, Z. R. Wasserman,L. A. Chung, W. F. DeGrado, Acc.
Chem. Res. 1993, 26, 191–197.
4. H. Bayley, Curr. Opin. Biotechnol. 1999, 10,94–103.
5. S. Lee, T. Kiyota, T. Kunitake, E. Matsumoto,S. Yamashita, K. Anzai, G. Sugihara,
Biochemistry 1997, 36, 3782–3791.
6.E. Matsumoto, T. Kiyota, S. Lee, G. Sugihara, S. Yamashita, H. Meno, Y. Aso,
H. Sakamoto, H. M. Ellerby, Biopolymers2001, 56, 96–108.
7.S. Cheley, O. Braha, X. Lu, S. Conlan,H. Bayley, Protein Sci. 1999, 8, 1257–1267.
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8. J.K. Percus, in: H.L. Frisch, J.L. Lebowitz (Eds.), The EquilibriumTheory of
Classical Fluids, W.A. Benjamin, New York, 1964, pp.
9. Vercoutere, W. et al. (2001) Rapid discrimination among individual DNA hairpin
molecules at single-necleotide resolution using an ionchannel. Nat. Biotechnol. 19,
248–252
10. Howorka, S. et al. (2001) Sequence-specific detection of individual DNA
strands using engineered nanopores. Nat. Biotechnol. 19, 636–639
11.Deamer, D.W. and Akeson, M. (2000) Nanopores and nucleic acids:
prospects for ultrarapid sequencing. Trends Biotechnol. 18, 147–151
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THANKS
FOR YOUR
PATIENCE
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