Nanopores promise cost savings in gene sequencing
(麻豆淫院)鈥擨n the last five years, next-鈥嬧�媑eneration gene sequencing has brought down the cost of unlocking a single genome from $10 mil颅lion to $10,000. While the sav颅ings is unprece颅dented, more can still be done to reduce the cost even fur颅ther, an effort that would enable a host of appli颅ca颅tions in med颅ical research and healthcare.
Meni Wanunu, an assis颅tant pro颅fessor of physics at North颅eastern Uni颅ver颅sity, says his work in nanopore sequencing rep颅re颅sents one such effort. Tra颅di颅tion颅ally, Wanunu has used nanopores as a DNA readout device, wherein a single strand of DNA passes through the pore causing minute changes to the sur颅rounding elec颅trical signal that reports on its structure.
But now he's doing the oppo颅site: "We'll use the nanopore to hold a mol颅e颅cule fixed in space," Wanunu explains.
Backed by a recent $825,000 grant from the National Insti颅tutes of Health, Wanunu will apply nanopores to another sequencing tech颅nology that reads exactly one strand of DNA at a time.
Pacific Bio颅sciences, Wanunu's grant partner, has designed a sequencing device called a SMRT Cell for single-鈥嬧�媘olecule, real-鈥嬧�媡ime analysis. SMRT cells have the poten颅tial to bring gene-鈥嬧�媠equencing costs down to $100 per genome, but they must first over颅come some sig颅nif颅i颅cant hurdles.
Each alu颅minum SMRT cell con颅tains 150,000 holes. Each hole is 100 nanome颅ters wide and should con颅tain one "poly颅merase," a mol颅e颅cule whose native respon颅si颅bility in a living cell is to repli颅cate a DNA sequence, one nucleotide base at a time. Poly颅merases are nature's best DNA sequencers and SMRT cells take advan颅tage of a mol颅e颅cule with mil颅lions of years of evo颅lu颅tion behind it.
But according to Wanunu, only about 37 per颅cent of the holes in a SMRT cell can the颅o颅ret颅i颅cally con颅tain exactly one poly颅merase, because there's no tech颅nology to put exactly one poly颅merase in each hole. While 100 nanome颅ters 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. Sit颅ting above the nanopore, each poly颅merase will be attached to an anchor below it, thus pre颅venting the former from floating away.
By ensuring that there is a single poly颅merase in each hole, the nanopore approach will increase the number of gene sequences that can be read at once, improving the overall yield of the SMRT cell. Addi颅tion颅ally, since nanopores are so small, it's pos颅sible to create a voltage gra颅dient across them, dri颅ving charged DNA strands toward the holes, and thus increasing the sen颅si颅tivity of the sequencer to DNA molecules.
"The niche here is sequencing native DNA that cannot be ampli颅fied," Wanunu says. Epi颅ge颅netic markers, for example, which sit on top of our genes and reg颅u颅late expres颅sion, are lost when DNA is ampli颅fied鈥攁 stan颅dard process in most sequencing tech颅nolo颅gies. By reading DNA one strand at a time, then, the SMRT cell would not only decrease costs but would also enable a new fron颅tier in genome research.
Provided by Northeastern University
