Nanopores promise cost savings in gene sequencing

September 20, 2012 by Angela Herring, Northeastern University
Assistant professor of physics Meni Wanunu uses nanopores to read a gene sequence one strand of DNA at a time.

(—In the last five years, next-​​generation gene sequencing has brought down the cost of unlocking a single genome from $10 mil­lion to $10,000. While the sav­ings is unprece­dented, more can still be done to reduce the cost even fur­ther, an effort that would enable a host of appli­ca­tions in med­ical research and healthcare.

Meni Wanunu, an assis­tant pro­fessor of physics at North­eastern Uni­ver­sity, says his work in nanopore sequencing rep­re­sents one such effort. Tra­di­tion­ally, Wanunu has used nanopores as a DNA readout device, wherein a single strand of DNA passes through the pore causing minute changes to the sur­rounding elec­trical signal that reports on its structure.

But now he's doing the oppo­site: "We'll use the nanopore to hold a mol­e­cule fixed in space," Wanunu explains.

Backed by a recent $825,000 grant from the National Insti­tutes of Health, Wanunu will apply nanopores to another sequencing tech­nology that reads exactly one strand of DNA at a time.

Pacific Bio­sciences, Wanunu's grant partner, has designed a sequencing device called a SMRT Cell for single-​​molecule, real-​​time analysis. SMRT cells have the poten­tial to bring gene-​​sequencing costs down to $100 per genome, but they must first over­come some sig­nif­i­cant hurdles.

Each alu­minum SMRT cell con­tains 150,000 holes. Each hole is 100 nanome­ters wide and should con­tain one "poly­merase," a mol­e­cule whose native respon­si­bility in a living cell is to repli­cate a DNA sequence, one base at a time. Poly­merases are nature's best DNA sequencers and SMRT take advan­tage of a mol­e­cule with mil­lions of years of evo­lu­tion behind it.

But according to Wanunu, only about 37 per­cent of the holes in a SMRT cell can the­o­ret­i­cally con­tain exactly one poly­merase, because there's no tech­nology to put exactly one poly­merase in each hole. While 100 nanome­ters may seem small, one of Wanunu's nanopores is 100 times smaller.

The goal of the research backed by the new grant is to match each SMRT cell hole with a single nanopore. Sit­ting above the nanopore, each poly­merase will be attached to an anchor below it, thus pre­venting the former from floating away.

By ensuring that there is a single poly­merase in each hole, the approach will increase the number of gene sequences that can be read at once, improving the overall yield of the SMRT cell. Addi­tion­ally, since nanopores are so small, it's pos­sible to create a voltage gra­dient across them, dri­ving charged DNA strands toward the holes, and thus increasing the sen­si­tivity of the sequencer to DNA molecules.

"The niche here is sequencing native DNA that cannot be ampli­fied," Wanunu says. Epi­ge­netic markers, for example, which sit on top of our genes and reg­u­late expres­sion, are lost when DNA is ampli­fied—a stan­dard process in most sequencing tech­nolo­gies. By reading DNA one strand at a time, then, the SMRT cell would not only decrease costs but would also enable a new fron­tier in genome research.

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