Next Generation DNA Sequencing Technologies

By Will Soutter

Topics Covered

Introduction
Nanopore Sequencing
Challenges to Development of Nanopore Technology
Nanotechnology in Other Next Generation Sequencing Techniques
Conclusions
References

Introduction

The ability to determine the sequence of base pairs in a strand of DNA is one of the most important techniques available to biomedical researchers. The most common techniques used today were first developed by Frederick Sanger in the 1970s.

Whilst well established, Sanger techniques remain costly and complicated to perform, which has limited their application beyond research.

More recently, various "next generation" sequencing technologies have emerged, which aim to increase the throughput and accuracy of DNA sequencing. This will allow sequencing to be applied in more widespread applications, particularly in the field of personalized medicine.

Some of these novel technologies rely on the understanding that nanotechnology research has provided. The ability to manipulate macromolecular DNA structures on the nanoscale has been exploited to create techniques which can sequence DNA much more rapidly than conventional Sanger techniques.

Nanopore Sequencing

Nanopore sequencing is the result of the miniaturization of sequencing technology down to the molecular level. DNA molecules are threaded through nanopores, usually either constructed from proteins or etched into silicon surfaces using nanofabrication techniques.

As the DNA strand passes through the nanopore, the current passing across the pore depends on which base is passing through at that moment. Monitoring the changes in current therefore produces a map of the base sequence.

Under normal circumstances, the DNA strand passes through the pore too quickly to obtain an accurate reading of the structure. Methods have therefore been developed to slow down the movement of the DNA molecules. These methods include attaching various chemical units to the DNA or to the pore to anchor the molecule, or to increase its affinity for the pore.

A more advanced technique which has emerged recently is to use DNA polymerase enzymes to drive DNA through the nanopore at a readable speed as it is synthesized. This limits the rate of DNA transfer through the nanopore to the speed at which it is processed by the enzyme - typically around 10ms per nucleotide, which is slow enough for the circuitry to gain an accurate reading of the ion current.

Figure 1. This video from Oxford Nanopore Technologies demonstrates their modular nanopore analysis systems, which can be calibrated to sequence DNA, RNA, proteins, and other molecules.

Challenges to Development of Nanopore Technology

One of the major promises that nanopore sequencing has made is to increase the read length - the number of base pairs that can be read from a single sample of DNA. This is a major limitation of conventional sequencing technologies, and would allow for much simpler sequencing, with less sample preparation and higher throughput. There is a challenge, however, is developing nanopore technology to take full advantage of its potential. There are many practical issues around high read-length sequencing which must be overcome, particularly if the technology has to be scaled to allow readily available, portable devices.

Another challenge which must be met before the next generation sequencing can be used in all the areas it has potential for is the nanopore fabrication. This is currently done with a number of different methods on a research scale, but many of the manufacturing techniques are not easy to scale up. Even the more conventional techniques like silicon nanofabrication have to stand up to the rigour of large-scale production equipment before the full benefits of nanopore sequencing will be achievable.

Nanotechnology in Other Next Generation Sequencing Techniques

Nanotechnology has also informed the development of alternative sequencing methods, although these have not received the same level of research attention as nanopore sequencing.

These other nanoscale sequencing techniques include diffusion of nucleotides labelled with fluorescent chemical tags through a zero-mode waveguide (an optical trap which is smaller than the wavelength of the light used in all three dimensions), or using DNA polymerases modified with quantum dots.

These techniques could drastically improve the throughput and efficiency of sequencing, although they are effectively improvements on existing Sanger techniques, rather than new approaches like nanopore sequencing.

Figure 2. This video from Pacific Biosciences explains their proprietary technology, using fluorescent tags to sequence DNA as it is synthesized by DNA polymerase.

Conclusions

Next generation sequencing technologies - in particular nanopore sequencing - have the potential to revolutionize the field of genomics, and the wider world of medicine. Unlike many other novel nanotechnologies, the barriers and challenges which may slow the commercial adoption of nanopore sequencing appear to be surmountable. Indeed, some companies, like Oxford Nanopore Technologies and Pacific Biosciences, have already brought nanopore and other next-generation sequencing devices to market.

References

  • "Briefing: Next Generation Sequencing" - EU ObservatoryNano
  • "The potential and challenges of nanopore sequencing" - Branton et al, Nature Biotechnology 2008. DOI: 10.1038/nbt.1495
  • "DNA sequencing with nanopores" - G.F. Schneider and C. Dekker, Nature Biotechnology 2012. DOI: 10.1038/nbt.2181
Date Added: Aug 30, 2012 | Updated: Aug 30, 2012
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