DNA sequencing in zero gravity with handheld nanotech

Nanotechnology. When American engineer Eric Drexler coined this futuristic term in 1981, he had in mind molecule-sized machines that would do useful tasks. The idea was to copy nature’s own machines – muscle proteins that exert force, for instance, or enzymes that carry out chemical reactions. But engineering at the nanometre scale is tough. We are talking about working with individual atoms. A silicon atom is 0.2 nanometres across. A muscle protein filament is as little as 7 nanometres in diameter. 

For decades, we let human engineers off the hook, allowing a bevy of prosaic items from paints to plastics to claim the title of nanotechnology. To qualify, these products just had to involve particles smaller than 100 nanometres and display novel properties.

But finally, last year, a man-made machine claimed the title in the way Drexler imagined. It also made it into the top 10 list of Science magazine’s breakthroughs of the year. 

Delightfully, this nano machine made by Oxford Nanopore Technologies mimics nature to achieve the feat of reading the sequence of the letters of the DNA code, the chemical bases guanine, adenine, thymine and cytosine.

The machine is the size of a mobile phone and, unlike traditional sequencers which are desktop-sized and require the DNA to be pre-cut into short segments, it can handle DNA as it comes: double-stranded, long threads. 

This “pocket sequencer” promises to make DNA sequencing cheaper and more accessible. It has already been used to identify the Ebola virus in a matter of hours and to read the sequence of soil microbes aboard the International Space Station. 

Here’s a nutshell description of how the sequencer works. 

The machine is a “nanopore”, a large single molecule pierced by a hollow channel a couple of nanometres in diameter. If you embed this nanopore in an ultrathin membrane bathed in an ionic solution and apply a small voltage, a tiny current will flow. 

(As an aside, the reason I am so tickled by this achievement is that our brain cells also communicate via tiny currents flowing through the pores of proteins called ion channels; I spent the major part of my working career designing and manufacturing sensitive amplifiers to measure these currents.) 

The simple idea behind the nanopore is that as a strand of DNA is threaded through, it partially blocks the current flow. Since the degree of blockage depends on the particular DNA letter, the fluctuations in the current pattern reflect the sequence of letters on the DNA strand as it slithers through the nanopore.

Sounds simple but, as always, the devil is in the detail. 

The nanopore has two modules. The first grabs double-stranded DNA, cleaves away one of the strands, then ratchets the remaining single strand into and through the hole. It holds each base for a hundred microseconds or more before allowing it to proceed, thereby giving the detection system time to make its measurements. 

The second component is the pore. Shaped like a thin hourglass, at its narrowest it is a mere 1.2 nanometres in diameter. This narrowing is the sensing region where the electrical resistance changes as each base squeezes through. {%recommended 895%}

A complication is that neighbouring bases on the DNA strand can partially block the constriction. Accuracy is restored by reading the DNA strand multiple times. 

Ingenious, but it took 25 years to master these devilish details. The implausible idea for nanopore sequencing was conceived in 1989 by David Deamer from the University of California at Santa Cruz; but it was way ahead of its time. 

Years later I was delighted to learn that Deamer and his colleagues, in their early experiments to detect the resistance fluctuations, used a “patch clamp” amplifier made by my former company, Axon Instruments.

How does Oxford make the nanopores? It programs bacteria to do the work. Now scientists there and elsewhere are trying to develop next-generation nanopores that will be directly fabricated from silicon nitride or graphene molecules. If they succeed, that will truly be Eric Drexler’s dream fulfilled.