Solid State Nanopores for Selective Sensing of DNA - Nanopores: Sensing and Fundamental Biological Interactions - page 122

with gold nanotubes [ 55 ]. They functionalized the membrane pores with specific
DNA hair-pin probes and used it for selective DNA translocation. They referred
to their hair-pin loop DNA as “transporter”. They found different fluxes for perfect
complementary (PC) DNA and single-base-mismatch (SBM) DNA target molecules.
Similar results have been reported by others as well [ 56 ]. Peptide nucleic
acids (PNA) were used as probes by one group [ 57 ]. PNA molecules are uncharged,
synthetic DNA analogs. They gave better ionic strength dependant hybridization
and biochemical stability. When PNA molecules were attached as probe to the
nanopore walls they give more flux modulation on translocation of complementary
DNA sequence. The increased flux modulation was the result of the charge
repulsion mechanism when complementary DNA ( ve charge) hybridized to
PNA (uncharged). At higher electrolyte concentrations, decreases in flux were not
distinguishable. At much lower concentrations, the pore gave one fold modulation
of flux upon DNA-PNA binding.
Using biological ion channel -HL), discrimination between

complementary DNA and single base mismatch targets has been reported
before [ 31 , 58 ]. A longer translocation time was reported when a PC target passed
through the

a -Hemolysin ( a

-HL channel as compared to a single base mismatched DNA target.
Iqbal et al. used functionalized Si nanopores and reported the change in trans-
location time based on target DNA sequence, but interestingly they found longer
translocation pulses for SBM ss-DNA sequences [ 1 ]. The nanopore surface
was functionalized with hair-pin loop DNA as a selective probe. The fabricated
nanopore and functionalized nanopore schematic is shown in Fig. 5.8 . PC and

a

Fig. 5.8 The nanopore diameter functionalized with hairpin-loop probe DNA. The nanopore diame-
ter was 16-18 nmwhich reduced to 2 nm after hairpin-loop immobilization inside the pore. Reprinted
by permission fromMacmillan Publishers Ltd: Nature Nanotechnology, copyright (2007)