Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 263

Fig. 11.9 Scatter plots of amplitude and duration of current blockades caused by RNA homo-
polymers passing through the alpha-HL pore. Typical blockade events comprising each plot are
shown on the right. ( Top ) Blockades caused by poly(A) (150 nucleotide nominal length,
200 mgml 1 ). ( Middle ) Blockades caused by poly(C) (125 nucleotide nominal length, 200 mgml 1 ).
( bottom ) Blockades caused by a mixture of poly(C) (125 nucleotide nominal length) and poly(A)
(175 nucleotide nominal length). Quiescent periods between events were spliced out of the plots on
the right so that numerous blockades could be presented in one figure. Image adapted from [ 13 ]
The first lesson one can learn from this experiment is that the secondary structure
of DNA has to be eliminated for the purpose of sequencing DNA. As suggested by
Kasianowicz et al . [ 11 ], at least four conditions have to be met for this nanopore
DNA sequencing method to be possible:
1. The channel and membrane must be sufficiently robust to withstand whatever
temperature and chemical treatments are required to eliminate interference from
polynucleotide secondary structures;
2. The length of the nanopore channel has to be comparable with the inter base
distance of 0.4 nm;
3. Each nucleotide must produce a characteristic transient current blockage;
4. The rate of nucleotide movement through the channel must be slower than the
time resolution of ionic current measurement system.