Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 118

a b c

Electric Field applied vs. Effective Pore Size

22

21

Effective diameter

20

B

19

18

17

16

15

14

10 15 20 25 30 35 40

Electric Field (kcal/mol.A.e)

Fig. 5.7 The ss-DNAs coated on nanopore surface. (a) Radii of gyration for same length ss-DNA
in hairpin and linear conformation, coated inside a pore; (b) Effective pore diameter; (c) DNA re-
orients under applied electric field of various strengths and effective pore diameter as a function of
electric field strength. The plot in (c) shows the linear effect of electric field on the pore diameter.
This type of estimation is very important in determining the optimal condition of DNA analysis.
Reprinted by permission from New World Publishing International: American Journal of Biomed-
ical Sciences, copyright (2009)

5.4 Selective DNA Translocation

Functionalizing the inner nanopore walls is essential for selective DNA trans-
location. The nanopores can be chemically modified for bio-sensing [ 32 - 36 ].
For selective nanopore sensing, we have to not only provide selective probes but
also have to control the surface charges and hydrophobicity of the nanopores.
Surface charges play very important role in determining the ionic current and
DNA interactions during translocation [ 37 ]. The surface modification improves
the physicochemical properties and is the basic approach for selective sensing.
Selectivity of nanopore transport channels can be controlled with a tethered
ss-DNA attachment for selective molecular recognition [ 38 ]. Based on the material
in which the SSN is fabricated, different strategies are employed depending on
the surface functionalities of nanopore. The second goal to functionalize the
nanopore is to make it more biologically friendly.

5.4.1 Functionalization, Sensing and Selectivity

Polymer deposition as described in Sect. 2.1.2 forms the basis for functionalization
of the solid state nanopore. Depending on the substrate material and target mole-
cules, different approaches are used for surface modification. Siwy et al. explored
the thiol chemisorption on the gold surface of nanotubes [ 39 ]. They suggested
an abiotic mimic with a single conical gold nanotube in a synthetic membrane.