Rational Design for Cooperative Recognition of Specific Nucleobases Using β‐Cyclodextrin‐Modified DNAs and Fluorescent Ligands on DNA and RNA Scaffolds |
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Authors: | Akika Futamura Asuka Uemura Takeshi Imoto Dr Yusuke Kitamura Dr Hirotaka Matsuura Dr Chun‐Xia Wang Toshiki Ichihashi Dr Yusuke Sato Prof?Dr Norio Teramae Prof?Dr Seiichi Nishizawa Prof?Dr Toshihiro Ihara |
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Institution: | 1. Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Kurokami, Chuo‐ku, Kumamoto 860‐8555 (Japan), Fax: (+81)?96‐342‐3679 (office) or 3873;2. CREST Japan Science and Technology Agency, Gobancho, Chiyoda‐ku, Tokyo 102‐0076 (Japan);3. Department of Chemistry, Graduate School of Science, Tohoku University, Aoba‐ku, Sendai 980‐8578 (Japan) |
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Abstract: | We propose a binary fluorimetric method for DNA and RNA analysis by the combined use of two probes rationally designed to work cooperatively. One probe is an oligonucleotide (ODN) conjugate bearing a β‐cyclodextrin (β‐CyD). The other probe is a small reporter ligand, which comprises linked molecules of a nucleobase‐specific heterocycle and an environment‐sensitive fluorophore. The heterocycle of the reporter ligand recognizes a single nucleobase displayed in a gap on the target labeled with the conjugate and, at the same time, the fluorophore moiety forms a luminous inclusion complex with nearby β‐CyD. Three reporter ligands, MNDS (naphthyridine–dansyl linked ligand), MNDB (naphthyridine–DBD), and DPDB (pyridine–DBD), were used for DNA and RNA probing with 3′‐end or 5′‐end modified β‐CyD – ODN conjugates. For the DNA target, the β‐CyD tethered to the 3′‐end of the ODN facing into the gap interacted with the fluorophore sticking out into the major groove of the gap site ( MNDS and DPDB ). Meanwhile the β‐CyD on the 5′‐end of the ODN interacted with the fluorophore in the minor groove ( MNDB and DPDB ). The results obtained by this study could be a guideline for the design of binary DNA/RNA probe systems based on controlling the proximity of functional molecules. |
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Keywords: | biosensors cyclodextrin DNA recognition fluorescence host– guest systems |
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