Controlling the Fluorescence of Benzofuran‐Modified Uracil Residues in Oligonucleotides by Triple‐Helix Formation |
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| Authors: | Dr Takashi Kanamori Hiroki Ohzeki Dr Yoshiaki Masaki Prof Akihiro Ohkubo Mari Takahashi Kengo Tsuda Dr Takuhiro Ito Prof Mikako Shirouzu Dr Kanako Kuwasako Prof Yutaka Muto Prof Mitsuo Sekine Prof Kohji Seio |
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| Affiliation: | 1. Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226‐8501 (Japan);2. Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226‐8501 (Japan);3. RIKEN Systems and Structural Biology Center, 1‐7‐22 Suehiro‐cho, Tsurumi, Yokohama 230‐0045 (Japan);4. RIKEN Center for Life Science Technologies, 1‐7‐22 Suehiro‐cho, Tsurumi, Yokohama 230‐0045 (Japan);5. Faculty of Pharmacy, Department of Pharmaceutical Sciences, Musashino University, 1‐1‐20, Shinmachi Nishitokyo‐city, Tokyo 202‐8585 (Japan) |
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| Abstract: | We developed fluorescent turn‐on probes containing a fluorescent nucleoside, 5‐(benzofuran‐2‐yl)deoxyuridine (dUBF) or 5‐(3‐methylbenzofuran‐2‐yl)deoxyuridine (dUMBF), for the detection of single‐stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dUMBF achieved superior fluorescence enhancement than that containing dUBF. NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3‐methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3‐methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex‐induced fluorescence enhancement of the oligonucleotide probe containing dUMBF. |
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| Keywords: | DNA structures fluorescent probes NMR spectroscopy RNA sensors |
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