2007 Fiscal Year Final Research Report Summary
Studies of elementary techniques for developing on-chip devices for single genomic DNA manipulation and analysis
| Project/Area Number |
17310081
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Microdevices/Nanodevices
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| Research Institution | The University of Tokyo |
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Principal Investigator |
OANA Hidehiro The University of Tokyo, Graduate School of Engineering, Lecturer (20314172)
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| Co-Investigator(Kenkyū-buntansha) |
WASHIZU Masao Kyoto University, Graduate School of Medicine, Associate Professor (10201162)
加畑 博幸 京都大学, 医学研究科, 科学技術振興准教授 (70293884)
WASHIZU Masao The University of Tokyo, Graduate School of Enginering, Professor (10201162)
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| Project Period (FY) |
2005 – 2007
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| Keywords | DNA / single molecule analysis / micro manipulation / optical tweezers / micro fluidic devidce |
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| Research Abstract |
Through this research, we developed a new methodology for the observation and the artificial control of higher-order structures of genomic DNA molecules, and the method enables reversible folding and unfolding of over 250 μm-long DNA with a high reproducibility.
In eukaryotic cells, DNA with the aid of cationic proteins such as histone are folded to form a highly ordered chromosome structures, and the gene expression is influenced by how tightly it is fold around a particular gene, which is controlled by such a process as histone methylation or acetylation. However, the mechanism and the dynamics of DNA folding, such as the speed of folding on a DNA strand, or how much cooperativity (the folding speed is enhanced once folding starts) influences the folding of very long DNA strand, is not well understood.
Such a study requires a method to stretch DNA strands, hold it in a solution, which can be quickly replaced the solutions having different cationic or salt concentrations. For this purpose, we have developed a microfluidic device. The device which we developed is fabricated by a standard soft lithography with PDMS. The main channel of the device has micro-pillars to hook and stretch DNA by hydrodynamic force. There are inlets on the upstream side of the pillars, from which yeast chromosomal DNA, 1 mM spermidine (DNA condensing polycationic agent), and 500 mM NaCl (de-condensing salt) are fed. Each solution contains 1 μM YO-PRO-1 for fluorescent visualization of DNA.
The method developed here not only contributes to the basic biochemical researches, but may also open a way for the DNA handling towards single-molecule sequencing, or control of cellular activity through artificially induced higher-order changes.
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