image: This is a typical nanopore sequencing process. view more
Credit: ©Science China Press
DNA sequencing seems to be an eternal theme for human due to the desire of ascertaining the nature of life. Professor QIAN Linmao and his group from Tribology Research Institute, Southwest Jiaotong University were working on the optimization of the third-generation sequencing technique based on nanopore. They found that long chain DNA with low salt concentration is more conducive to the nanopore sequencing process. Their work, entitled "Effect of chain length on the conformation and friction behaviour of DNA", was published in SCIENCE CHINA Technological Sciences. 2013, Vol 56(12).
When Watson and Crick proposed the double helix structure of DNA in 1953, a significant era was opened for a new stage of the life sciences. Since the detection of DNA sequence can help people prevent and treat many genetic diseases, DNA sequencing technology has been one of the important means of modern biological research. The first-generation sequencing was proposed in the 1970s, by which it took more than 10 years and $1 billion to complete the Human Genome Project. In 2005, the second-generation sequencing technology was developed, by which the sequencing period for individual human genome could be reduced to be only 1 week. In recent years, the third-generation sequencing based on nanopore has been widespread concerned as a potential candidate for achieving the ''$1000 genome'' goal set by the US National Institutes of Health.
In a typical nanopore sequencing process, when a DNA molecule passes through a nanopore, a characteristic blockade ionic current can be detected to determine the information of the DNA molecule (shown in the image). It exhibits many advantages, such as accurate, rapid, low-cost and so on. Nevertheless, there are several challenges in nanopore sequencing. For example, the coiled conformation of a DNA molecule makes it difficult for one end of a DNA molecule to reach into a nanopore, and the high translocation speed made it extremely difficult to distinguish the desired current signal. Therefore, it is essential to solve the problem and improve the nanopore sequencing technique.
In August 2013, Professor Qian and his team reported that, low salt concentration is more conducive to the sequencing process, since it can not only make DNA molecules easier to reach into nanopore through extended conformation, but also reduce the passage rate by high friction between DNA molecule and the wall of nanopore. In the present study, the team confirmed that, with the increase of chain length, the DNA molecule became more extended, which can make DNA molecules reach into and pass through the nanopore readily. Additionally, the effect of chain length on the friction of DNA was insignificant under low normal load which indicated that the nanopore sequencing technique was not restricted by the chain length of DNA molecules. In summary, long chain DNA with low salt concentration is more conducive to the third-generation sequencing technique based on nanopore and the expectation of longer reads could be realized in the future.
"In the future, everyone could afford to carry out their own gene sequencing," Qian says, "Based on our results, the nanopore sequencing technique is not restricted by the chain length of DNA molecules. It may improve the efficiency of sequencing, which means that the cost of gene sequencing could be further reduced."
On the strength of these findings, the researchers are beginning an extensive project to optimize the parameters in the third-generation sequencing. The results will benefit the development of third-generation sequencing, but the benefits will likely extend further, Qian says.
"There is much more beyond optimization of the nanopore sequencing," Qian says, "A lot of basic research needs to be done and we will work on it."
Corresponding Author：
QIAN Linmao
linmao@swjtu.edu.cn
See the article: Wang M, Cui S X, Yun B J, Qian L M. Effect of chain length on the conformation and friction behaviour of DNA. SCI CHINA Tech Sci, 2013 Vol. 56 (12): 2927-2933
http://tech.scichina.com:8082/sciEe/EN/abstract/abstract512538.shtml
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