Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 268

Fig. 11.15 Voltage traces due to translocation of single bases C, A, T and G. The inset illustrates
the conformations of the replaced nucleotides. The orientations of their aromatic rings as well as
the backbone structures are identical. Image adapted from [ 24 ]
11.1.4.4 Nanopore-Based DNA Sequencing via Unzipping
Designed DNAs
Quite different from the above electronic detection approaches, this proposal [ 22 ]is
based on the detection of optical signals while a designed DNA is unzipped by a
nanopore, as shown in Fig. 11.16 . A biochemical process is employed to create the
designed DNA [ 22 ]. The DNA molecule to be sequenced is recoded in such a way
that each nucleotide in the original DNA is represented by 20-base sequences in the
designed DNA. The 20-base sequences are two blocks of 10-base strands and each
10-base strand has two variations, which can be used to code the four different bases
A, T, C, G in the original DNA. The two variations of the 10-base strands are each
labeled with a different fluorescent tag on one end and a quenching molecule at the
other end. In a double strand designed DNA, a quenching molecule is always close
enough to a fluorescent tag, which prevents detecting the fluorescence from
the background fluorescent tags. The fluorescence signal can only be detected at
the entrance of the nanopore when the quencher is pulled away from the fluorescent
tag during unzipping of the ds-DNA by the nanopore [ 25 - 27 ], as the oligomers
complementary to the 20-mers coding each nucleotide form a stem-loop structure in
which the quencher/fluorescent pairs are in close proximity (Fig. 11.16 ). Although
this method requires some biochemical process, it is still a very promising near-term
DNA sequencing technology, as it can be parallelized by using nanopore arrays.