Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 269

Fig. 11.16 Schematic of the
concept of nanopore DNA
sequencing via unzipping
designed DNAs. (Courtesy
of A. Meller)

11.1.4.5 Hybridization-Assisted Nanopore DNA Sequencing

To overcome two of the current difficulties in nanopore DNA sequencing: fabricating
a nanopore with length comparable with the length of a single base and detecting
the characteristic transient current blockages of single DNA bases, Ling et al . [ 23 ]
proposed the Hybridization-assisted Nanopore DNA Sequencing (HANS) method.
The principle of this proposal is shown in Fig. 11.17 . An insulating solid state
nanopore membrane (shown in gray) separates two ionic buffers. The unknown single
strand DNA is shown as the top strand in the figure. Short known oligonucleotides
(DNA probes, shown as the bottom strands in the figure) are annealed onto their
complimentary part of the single stranded template DNA. The single stranded DNA
with hybridized probes is then driven through the nanopore by applying a voltage bias
across the nanopore. The expected ionic current trace due to the blockage of the single
strand part and the double strand part of the DNA is shown in the lower panel of the
figure. In this way, one only needs to detect the ionic current differences between the
single strand part and double strand part of the DNA, thus bypassing the difficulty to
detect the transient current differences between single DNA bases in the original
KBBD proposal. Additionally, one only needs to detect ionic current signals of
oligonucleotides instead of single bases, thus bypassing the difficulty of fabricating
a nanopore with length comparable with the length of a single base.
Sequencing by hybridization (SBH) [ 29 , 30 ] is currently not competitive for
sequencing as it cannot detect the repeats of DNA probes, which limits the ability to
have the complete information needed for reconstruction of the DNA sequence. By
combing SBH with the nanopore technology [ 4 ], one can detect the repeating DNA
probes as well as the location of the probes from the ionic current trace. For probe
length n , one simply tries all 4 n possible probes separately and records the