Biomedical Engineering Reference
In-Depth Information
that the ionic current versus time trace should reveal two features corresponding
to the two matching oligonucleotides. The sequencing is achieved by aligning the
current blockades signals and their corresponding probe sequences similar to
the concept of sequencing by hybridization (SBH). The key difference between
HANS and SBH is that the main framework of sequence information in HANS
is formed by the locations of the DNA probes, thus free from the problems of repeat
sequences in a DNA.
The major difference between the HANS approach and that of the direct
nanopore sequencing of Kasianowicz et al. [
1
] is that the HANS approach bypasses
the harsh requirement of single-base spatial resolution (0.4 nm) which is smaller
than the pore length for both solid-state and biological nanopores.
8.4.2 Error Analysis of Positional Measurement Using DNA
Translocation Through a Nanopore
Even with the relaxed demand for positional accuracy in the HANS approach, it is
still worthwhile to consider the major obstacles. The first concern is that DNA
molecules are entropic springs (Marko and Siggia [
21
]), as such their contour
confirmation fluctuates violently at ambient temperatures. Fluctuations between
possible polymer configurations change the effective distance between the probes
on the ssDNA seen by the nanopore. The simplest solution will be to hold the DNA
under tension: the electric field inside the pore pulls the DNA forward, while the
magnetic force or optical force pulling on the bead backward, as shown in Fig.
8.10
.
Fig. 8.10 A simple model
for controlled DNA
translocation. The long black
lines are target ssDNA
molecules with unknown
sequences. The shorter bars
indicate two sets of
oligonucleotides with known
sequences from a n-mer
hybridization library. The
basic issue is whether the
nanopore technique is
ultimately capable of
resolving the difference
in their positions
Search WWH ::
Custom Search