FUJIMOTO Laboratory
<Major Research Areas>Bioorganic Chemistry, Nucleic Acids Chemistry, Chemical Biology

Photochemical DNA Manipulation

Research activity

1Photo-triggered DNA Manipulation

　　DNA engineering, the basis of modern protein engineering, has been developed since the 1960s with many discoveries, including those of various restriction enzymes and polymerases, and has produced a number of Nobel laureates for their contributions to, for example, the PCR method or DNA sequencing method. The existing biotechnology is thus essential to basic research in the present DNA analysis or biochemistry. While many methods for enzymatic and chemical ligation of DNA fragments via a native phosphodiester bond or non-native linkages have been demonstrated, there are only a few methods for photoinduced non-enzymatic chemical ligation. The merit of the photochemical ligation avoiding the need for additional reagent is obvious. Furthermore, their actions are controllable within space and time by the choice of proper irradiation methods. The photoligation methods can be used as a tool for DNA engineering and nanotechnology, and as photoregulated diagnostic and therapeutic agents. Therefore, the target in my research is the development of phototriggered DNA manipulation via intelligent nucleic acids toward next generation DNA manipulation.

2Development of Intelligent DNA

　　Based on precise molecular design with molecular calculations, we have been accurately synthesizing highly functional nucleic acids with the help of organometal chemistry. We have also been developing intelligent nucleic acids that have novel functions and are trying to apply them to new molecular devices, new molecular sensors, or new materials. To be more specific, we focus on the development of functional intelligent nucleic acids for various purposes, such as conductive DNA wires, DNA sensors that detect target genes, light-writing DNA memories, and DNA computing with parallel processing DNA elements.

3Construction of DNA Nano-architechture

　　Our group has succeeded in developing the base unit of artificial nucleic acid structures, such as branch DNA, catenane DNA, cap DNA, and clip DNA. Generally, these are extremely difficult to develop with conventional enzyme methods. By creating DNA nano-architecture with these new secondary or tertiary structures, we expect that novel structure-dependent physical properties will appear, as we observe in RNA.

Equipment

DNA Synthesizer･MALDI-TOF MASS･UV･HPLC･Molecular Modeling System･Tm Analyzer

The main research achievements in the past five years

1. K. Fujimoto, T. Sakamoto, K. H. Hiratsuka and Y. Yoshimura, Site-Specific Photochemical RNA Editing, Chem. Commun. 46, 7545-7549 (2010).
2. Y. Yoshinaga, T. Ohtake, and K. Fujimoto, A new approach for reversible RNA photocrosslinking reaction: Application to sequence-specific RNA selection, ChemBioChem, 10, 1473-1476 (2009).
3. S. Ogasawara, T. Ami, and K. Fujimoto, Autonomous DNA computing machine based on photochemical gate transition, J. Am. Chem. Soc., 130, 10050-10051 (2008).
4. M. Ogino and K. Fujimoto, Photochemical synthesis of R-shaped DNA toward in vitro DNA recombination and processing, Angew. Chem. Int. Ed., 45, 7223-7226 (2006).
5. K. Fujimoto, Minister Award for Distinguished Young Scientists (Ministry of Education, Culture, Sports, Science and Technology, Japan) (2009)