Noblegen Biosciences is developing a single molecule sequencing technology that uses nanopores for the sequencing readout. However, rather than sequencing native DNA, the DNA is converted (through a process called ‘circular DNA conversion’) into a longer ‘expanded synthetic representation’ (ESR) molecule. In the ESR each original base is represented by a predefined unique sequence of nucleotides, each of which has a corresponding complementary color-coded ‘beacon’ with a fluorophore at one end and a quenching molecule on the other. The ESR is tagged with the beacons through hybridization, creating a double stranded molecule. In this arrangement, the fluorophores and quenchers of adjacent beacons are in proximity, so there is no fluorescent signal given off. The ESR-beacon complex is then pulled through a solid state nanopore, one molecule at a time. Due to the size restriction of the nanopore, the beacons are stripped off during this process. As the beacons come off, the fluor becomes unquenched and a flash of color coded light is emitted, recorded and translated into sequence. They call this process ‘Optipore’ (for optical nanopore) sequencing.
While they haven’t released any real specifications for their ‘low cost’ system, Noblegen speculates they could scale up to a 400 x 400 nanopore chip capable of generating 500 Gb/hr (which translates to one 30X-coverage genome every 15 minutes). Because of the conversion process, the initial reads are limited to ~200b. Their current plans are to target the diagnostic market with their Optipore system.
Key Paper: McNally, B., A. Singer, Z. Yu, Y. Sun, Z. Weng, and A. Meller. (2010) Optical Recognition of Converted DNA Nucleotides for Single-Molecule DNA Sequencing Using Nanopore Arrays. Nano Letters 10(6) 2237-44.
Projected Commercial Availability: 2014
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