Last updated on April 17, 2014 at 13:35 EDT

Hurdles Still Exist In Genomic Nanopore Sequencing

October 19, 2012

Alan McStravick for redOrbit.com – Your Universe Online

With the introduction of the idea of nanopore sequencing first being proposed in the mid 1990´s, huge advances have been made in this burgeoning technology. The strength of the idea lies in its simplicity. Nanopore sequencing is derived through the collection of a single thread of DNA which is passed through a tiny molecule-sized hole, or nanopore, allowing for the various DNA bases to be analyzed and identified as they move through the pore.

A new study has addressed the claim that nanopore technology is advancing so quickly that it is on the verge of making DNA analysis so fast and inexpensive that a person´s entire genome could be sequenced in just minutes and at a fraction of the cost. This idea has attracted interest among academic, industrial and commercial concerns. The new study published in a special issue of Physics in Life Reviews addressing nanopore sequencing specifically, questions whether the remaining technical advancements can be achieved in order to produce a workable, easily manufactured commercial device. This study was authored by Northeastern University physicist Meni Wanunu.

One of the companies that is pioneering sequencing technologies, Oxford Nanopore Technologies, earlier this year announced they expect nanopore strand sequencing to be able to produce a genomic map in 15 minutes at a cost of $1500 by 2014. Held in contrast to the $10 million price tag for the same results just 5 years ago, and it´s clear we are progressing at breakneck speeds in this field.

However, the reality of manipulating technology based on pores so tiny that 25,000 of them can fit side by side on a human hair has proved a daunting task, according to Wanunu. The primary challenge has been to slow the process down and control the movement of the DNA strand through the pore at a rate slow enough to make individual DNA bases readable and usable. There has been an attempt at a new approach that utilizes enzyme-controlled movement. It was designed specifically to aid in slowing the process. However, it has its own drawbacks, notably poor enzyme activity that results in limited processivity and also uncontrolled forward-reverse motion.

Also on the topic of setbacks is whether protein or solid-state pores provide the most promising technique. The naturally occurring porous proteins were initially investigated. The early 2000´s brought in what was considered to offer a better capability and flexibility through various solid-state nanopores that were made of silicon and graphene. “Since both lipid-embedded protein channels and solid-state nanopores have drawbacks, it will be interesting to see which device, or what combination of devices, will be available in years to come, if any,” Wanunu says.

He goes on to say that at this time there are still several hurdles to overcome, including the inability of nanopores to provide any spectroscopic information about the identity of a molecule, uncertainties about whether translocation occurs at a constant speed and the complications of pore clogging.

Published in the same journal issue as the study, John Kasianowicz from the National Institute of Standards and Technology in the US, and a pioneer in this field, wrote a comment that agrees that plenty of challenges remain. In his comment he said, “There are indeed still many problems to address in order to enable practical electronic nanopore-based sensing devices. However, by better understanding the road already developed in this nascent field, the journey will hopefully appear a little less daunting.”

Another comment on Wanunu´s review, offered by founder and Director of Oxford Nanopore Technologies, Hagan Bayley, looks more positively on the future. In his comment he said, “In the longer term, by using solid-state pores“¦it may be possible to read DNA sequences at microseconds rather than milliseconds per base. This could be done by using tunneling currents or other characteristics of the DNA bases for which graphene — with its unusual electronic properties — might after additional development provide a superior substrate and in so doing deliver another massive leap forward on top of a decade of unprecedented progress.”

Both the study and the comments made on its behalf have differing views on how the future of this field will progress. But with history in the rearview mirror, it is clear that we are on the precipice of the next big advancement in nanopore technology.

Source: Alan McStravick for redOrbit.com - Your Universe Online