Biomod/2012/Titech/Nano-Jugglers/Methods/DNA Design

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0.2. Design of linker DNA strands

    We used DNA strands for bonding between a body of Biomolecular Rocket and platinum particles. DNA strands must be designed 4 DNA strands to hybridize at room temperature stably. DNA strands are categorized into two types, one type was a DNA strand for conjugation to polystyrene surface and its cDNA, and another type was a DNA strand for conjugation to gold surface and its cDNA. Each cDNA conjugated to platinum particles.
    In this section, we explain how we design DNA strands. There are three steps to design DNA strands, first step is selection of DNA strands , second step is adjustment of the number of bases and final step is design of cDNA strand. We used NUPACK[1] for these processes of DNA design. NUPACK is a software for the analysis and design of nucleic acid systems.
    First, we chosed DNA strands from a treatise[2]. In this step, we analyzed whether DNA could easily hybridize at room temperature stably. Then we selected two DNA strands. Secondly, we adjusted number of bases in order to make DNA easily dissociated when they introduced photo-switching systems. Finally, we design complementary DNA of each DNA strands, and modify amino group and thiol group as necessary.
Reference
    [1] NUPACK nucleic acid package. http://www.nupack.org/
    [2] Tetsuro Kitajima, Masahiro Takinoue, Ko-ichiroh Shohda, Akira Suyama. LNCS 4848, 119-129 (2008)
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