Nooma Bio

Nooma Bio, Inc. is a company in Santa Cruz, California, that is developing an electronic way to map long DNA molecules with two nanopores at once. It was spun out of Ontera in August 2020 and had by 2022 an exclusive license from the University of California, Santa Cruz to the "Dual-pore device" patent.^[1][2] Its instrument measures the distances between tags attached to a DNA molecule at chosen sequence motifs. The result is a map of landmarks along the strand, and most of the bases go unread.

Ontera announced the spinout on August 11, 2020. The new company was to use "two nanopores to control and map genomic and epigenomic features" on single, high-molecular-weight DNA molecules, with Ontera's chief executive and William Dunbar, Ontera's chief technology officer, leading it while keeping their roles. Ontera kept "single silicon-nanopore technology for in-field precision diagnostics".^[1] On March 7, 2022 Nooma announced a new chief executive, a veteran of DNA sequencing whose earlier employers included Agilent Technologies and Pacific Biosciences, together with a senior vice president of engineering and a vice president of product development.^[3]

The March 2022 release summarizes the platform. It traps long DNA molecules tagged with short oligonucleotides and scans them electronically, repeatedly, in seconds. It can tell tags at genomic motifs from tags at base modifications, which removes the conversion chemistries that next-generation sequencing needs to detect modifications.^[3]

The device in the company's 2022 paper is a borosilicate glass chip with a common chamber above two opposing nanofluidic channels. Two pores, 20 to 30 nm across, are milled with a focused gallium ion beam in a silicon nitride membrane about 30 nm thick, and they sit about 500 nm apart; the buffer is 2 M lithium chloride, and a run takes 7 µL of DNA at 1 ng/µL, with molecules longer than about 10 kb so that one strand can span the gap.^[2] The technique is molecular flossing: the two pores pull on the strand in opposite directions, and the voltages are flipped each time the count of tags passing the second pore reaches a set number.

The 2022 paper automated two further steps. Zooming out raises the number of tags scanned on a molecule, and recapture catches a molecule that has left the pores so that the same or another region can be read. Recapture increased the merged alignment length by 38 percent over single scans. The test was a heterogeneous mixture of fragments of the Escherichia coli chromosome, a genome of 4.6 million base pairs. After 5.6 hours of recording the maps covered 2,355 resolvable sites, 68 percent of the reference sites, at 3.1-fold coverage, including 133 intervals shorter than 200 base pairs, and the observed resolution between tags was 150 base pairs on engineered DNA and 166 base pairs on native fragments.^[2] The authors compare this with optical mapping, which has a 50 percent chance of resolving two fluorescent reporters within 1,000 base pairs, and say that "with an appropriately designed array" the method could allow human-sized genome and epigenome mapping.^[2]

Eight of the nine authors were employees of Nooma Bio. The ninth was at McGill University, Montreal.^[2] All work was privately financed except the tag-pair resolution measurements, which a public research grant paid for.^[2] Another company, Nabsys of Providence, Rhode Island, also maps genomes electronically with solid-state detectors.^[4]

Kent Kemmish, the founder of Molecular Reality Corporation, wrote about the 2022 paper in March 2026. He noted that the authors "didn't sequence the genome" but "were able to map the positions of large tags on the DNA", which he compared to "being able to see the continents of Earth from space".^[5] The post is summarized in Molecular flossing.

• List of nanopore companies
• Molecular flossing
• Ontera