In 2001, Hagan Bayley’s lab at Texas A&M demonstrated a limited sequencing method based on the observation that correctly and incorrectly paired DNA bases disrupted nanopore current to different extents. They tethered a short piece of DNA with a few unknown bases to the entrance of the nanopore, then added other short DNA strands with different bases at the position corresponding to the unknown base on the tethered strand. By looking at which base produced the disruption corresponding to a perfect match, they could guess the unknown nucleotide.
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the reason is that we have only one “kind” of match, and marking the end of the position is always correct. with arbitrary lookarounds, instead of marking the match ended here, you would have to mark the match for lookaround #7 ended here, and the match for lookaround #3 ended 5 characters ago, and the match for lookaround #12 ended 100 characters ago. i had a lot of temptation to support arbitrary lookarounds, and it really does seem like an easy fix at first glance, but the complexities arise much later in the match loop, and this is a good example of how some theory just does not hold up when you implement it. as a side note, we can actually loosen this restriction on R3 (above) which is still work in progress, but not R1, because R1 is the one that determines the start position of the match.
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