Decoding the Human Genome in an Hour (2011.2.7)
Professor Kwang Soo Kim has come forth with a revolutionary and unprecedented method for DNA sequencing that can potentially decode 3 billion pairs of human genes in an hour. The field of DNA sequencing caught the world’s attention when the Human Genome Project was successfully completed in 2003, and many developed nations have since been competing to develop ways to increase the speed of genetic sequencing and analysis. This research is closely related with treating intractable or rare diseases and therefore will have important implications for life science.
Professor Kim, well-known for being nominated as a National Scientist by the Korean government in 2010, formed a team with two PhD candidates Seung Kyu Min and Yeonchoo Cho and a POSTECH graduate and current KAIST Professor, Dr. Wooyoun Kim, and developed an ultrafast DNA decoding method.
While conventional methods typically take several weeks to decode DNA, Professor Kim and his colleagues were able to predict that the entire human genome could be decoded in just a matter of hours with their proposed technique. The team used the supercomputing facilities at KISTI (the Korea Institute of Science and Technology Information) to conduct simulations. The research team anticipates that further research and optimization of their sequencing method could even further reduce the decoding time to just several minutes.
The sequencing technique published in Nature Nanotechnology involves measuring the changes to the electrical conductivity of a graphene nanoribbon when it interacts with a DNA strand that flows through a nano channel. As displayed in figure 1, the graphene is a two-dimensional carbon allotrope where the carbon atoms form a beehive-like lattice. The graphite, widely used in the core of a lead pencil, is a multilayered structure where numerous graphene sheets are piled up on top of each other. Graphene caught the world’s attention in 2004 when Drs. Geim and Novoselov succeeded in extracting these single sheets of graphene from graphite, for which they won the Nobel Prize in 2010.
The excitement over graphene is largely driven by its potential for next generation electronic devices that stand to replace the ubiquitous silicon-based semiconductor electronics. Further, graphene retains the excellent mechanical and electronic properties of carbon nanotubes, while exhibiting additional unique phenomena inherent in the simple twodimensional structure with the thickness of just a single atomic layer. The term ‘nanoribbon’ refers to the graphene made into a thin band, and a nanoribbon as thin as one nanometer has already been synthesized experimentally in Germany.
Genes are the instructions that give organisms their particular characteristics, and are made of a length of DNA (deoxyribonucleic acid). The key components of DNA consist of the nucleobases adenine (A), cytosine (C), guanine (G) and thymine (T). The genetic information is encoded according to how these nucleobases are arranged.
Earlier on, the sequencing method for the next-generation has been proposed to be distinguishing between A, C, G and T by comparing the electrical current of each base while the DNA strand passes through a nano-sized hole, or comparing the current of ions that pass through the hole. However, this method falls short because it is difficult to distinguish between each nucleobase due to overlapping signals that result from significant orientational fluctuations of the nucleobases as they pass through the hole.
Professor Kim’s team observed that when a DNA strand passes through the nanochannel, each base becomes attached one-by-one to the surface of the graphene nanoribbon for just a fraction of a microsecond (10-6 seconds). They found that during this short time, each of the four types of bases modified the conductivity of the graphene in its own unique way, thus enabling the four bases to be individually distinguished. Further, the team came up with a new concept for twodimensional data processing to observe the variation of electrical conductivity and demonstrated how to analyze the complex signals from the two-dimensional conductance.
The robustness of their sequencing approach has attracted the attention of scientists at many of the world’s leading research institutes. Indeed, not only is their method ultra-fast, but it also abolishes the need for DNA amplification or optical labeling, which can be costly and pose a major bottleneck to the speed of conventional sequencing techniques.
Additionally, this research creates a synergy among three different fields of science, namely nanotechnology (molecular engineering of nanoribbons), biotechnology (analysis of gene sequencing), and information technology (two-dimensional electrical conductivity data analysis), and provides an excellent example for multi-disciplinary research that is becoming increasingly prevalent in modern scientific pursuits.
Professor Kim commented, “In the short term, our ultrafast and low-cost DNA gene sequencing analysis method can be applied to customized medical treatments, which is currently a popular topic. In the longer term, it may push us into an era of post-genomics, where various aspects can be analyzed by the genetic information of a human, such as personality, instinct, talent, or adaptability.”