What are the inherent challenges of exonuclease-based sequencing, the approach Seq was pursuing?
[At Seq, later renamed Praelux,] we demonstrated and published the single-molecule digestion of lambda-sized DNA molecules with lambda exonuclease; [this was] work published by Johannes Dapprich. Those enzymes, as they exist today, are perfectly capable of chewing up 50,000 bases of sequence in a totally processive fashion, and releasing those single nucleotides from a duplex strand of DNA. They will, in fact, do better than that. So the prospects for doing extremely long reads is very real — the challenge, obviously, is then detecting and identifying these cleaved single nucleotides [and] retaining the proper sequential order that they were released. Just like all enzymes, they are not perfect clocks, they don’t chew off a single base at precisely the same rate; they are context-dependent and secondary-structure-dependent. But for all practical purposes, they do the job. The optical methods that we were pursuing at Seq with technologies that are much older than what we have currently
