Reading DNA as it’s pulled through a small hole

A new technique makes it possible to discriminate between all four chemical bases (ACGT) in a DNA strand – ushering in a new era of genetic-based diagnostics and treatments.

DNA sequencing technology has been improving by leaps and bounds in recent years, with several techniques vying for supremacy. An upstart technology, called nanopore sequencing, looks ready to jump to the front of the pack. ScienceNOW reports.

Sequencing decodes thousands of genes simultaneously. And now, for the first time, researchers can continuously read the chemical letters of DNA as it travels through a tiny pore – paving the way for new machines to decode DNA like an announcer reading a ticker tape.

Most sequencing techniques require days: machines copy DNA strands and modify them with fluorescent labels to enable them to read DNA’s sequence letters, or bases.

Nanopore tech, on the other hand, sequences single unmodified DNA strands, making it the fastest and cheapest sequencing method on the market.

Back in 1996, scientists figured out how to drive DNA through proteins with tiny pores embedded in a film using electrical charge. As bases pass through the pore, they change the electrical charge, and electronics that can detect these changes help identify the bases. But DNA moves through the pore too quickly to read off all the bases in sequence.

Just 2 years ago, researchers added something to the setup: a protein called phi29 that loosely grabs onto a DNA strand as it moves through the pore.

Now, a team led by Jens Gundlach of the University of Washington incorporated that phi29 to their setup, which uses a different pore protein that’s more adept at identifying all four chemical bases.

The phi29 protein slows the DNA down – only 20 to 30 nucleotide bases move through the pore each second – making it possible to electrically identify each one as it passes.

In February, nanopore sequencing company Oxford Nanopore Technologies said it would be selling machines with thousands of nanopores running in parallel. By early 2013, a full genome can be sequenced in as little as 15 minutes for around $1,000. Although, people are still waiting for proof. (Gundlach’s work, however, is the first paper where somebody has actually sequenced DNA.)

And according to Global Information Inc., the DNA sequencing market is expected to double to $6.6 billion by 2016 – growing from nearly $3 billion in 2011.

The work was published in Nature Biotechnology this week.