Nanopore Sequencing - Background

Background

DNA could be passed through the nanopore for various reasons. For example, electrophoresis might attract the DNA towards the nanopore, and it might eventually pass through it. Or, enzymes attached to the nanopore might guide DNA towards the nanopore. The scale of the nanopore means that the DNA may be forced through the hole as a long string, one base at a time, rather like thread through the eye of a needle. As it does so, each nucleotide on the DNA molecule may obstruct the nanopore to a different, characteristic degree. The amount of current which can pass through the nanopore at any given moment therefore varies depending on whether the nanopore is blocked by an A, a C, a G or a T. The change in the current through the nanopore as the DNA molecule passes through the nanopore represents a direct reading of the DNA sequence. Alternatively, a nanopore might be used to identify individual DNA bases as they pass through the nanopore in the correct order - this approach has been shown by Oxford Nanopore Technologies and Professor Hagan Bayley.

The potential is that a single molecule of DNA can be sequenced directly using a nanopore, without the need for an intervening PCR amplification step or a chemical labelling step or the need for optical instrumentation to identify the chemical label. As of July 2010, information available to the public indicates that nanopore sequencing is still in the development stage, with some laboratory-based data to back up the different components of the sequencing method. Despite these advancements, nanopore sequencing is not currently commercially available, parallelized, routineized, nor cost-effective enough to compete with "next generation sequencing" methods. Nanopore-based DNA analysis techniques are being industrially developed by Oxford Nanopore Technologies (developing direct exonuclease sequencing and strand sequencing using protein nanopores, and solid-state sequencing through internal R&D and collaborations with academic institutions), NabSys (using a library of DNA probes and using nanopores to detect where these probes have hybridized to single stranded DNA) and NobleGen(using nanopores in combination with fluorescent labels). IBM has noted research projects on computer simulations of translocation of a DNA strand through a solid-state nanopore, but not projects on identifying the DNA bases on that strand.