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Narrowly distributed DNA scission on a microchip by transient extensional flow

Byunghang Ha

Korea Advanced Institute of Science and Technology
B.S. Mechanical Engineering, 2003

DNA fragmentation with low polydispersity is indispensible for the efficient and accurate DNA sequencing. A single long DNA chain has to be cut into small fragments ranging from about 50 to 1000 base pairs, because those sizes are only sequencible via current Sanger method-based technologies. The DNA to be sequenced is amplified about tenfold and then randomly cut into many small pieces. This amplification step is tedious but necessary to ensure accurate sequencing. The sequence information read from the fragments is put together to form a complete genome sequence by computer algorithms. A computer takes all the little puzzle pieces, discovers the overlapping fragments, puts them in the right order, and produces a single sequence code of the three billion base pairs of the human genome. DNA fragments of uniform length are much preferred because they contain enough overlapping sequence information to put them together correctly.

My research is to design and build a microchip that breaks DNA via a pressure-driven transient extensional flow. Stretching flow gives high propensity to the midpoint scission, which allows the size control of DNA fragments. By conferring microfabrication, I can freely implement various flow geometries on a transparent glass chip, which will help discern the critical parameters in DNA scission. I aim to develop a device that accurately controls the size distribution of DNA fragments. In addition to the experimental work, I aim to model the DNA scission in the transient extensional flow via Brown dynamics simulation.

For the videos below, the right video corresponds to flow at (1), the middle video corresponds to flow at (2), and the left video corresponds to flow at (3).

DNA sequencing research draws vast amount of funding from institutes such as NIH because it is expected to have us figure out the functions of each genes and eventually what changes from each mutation. This will help better understand the cancer, genetic diseases, evolution, and so on. Accurate, quick and inexpensive sequencing technology is the key to the success and the controlled DNA fragment is very important in the process. The technology can be used in the other polymers. Thinking about one type of polymer that we use a lot everyday - plastic, we expect that the detailed understanding of controlled polymer scission will be very useful in various fields.

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