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Nucleic Acids Research, 2001, Vol. 29, No. 6 e34
© 2001 Oxford University Press

Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer

Shinya Kurata1,2, Takahiro Kanagawa2,3,*, Kazutaka Yamada1, Masaki Torimura3, Toyokazu Yokomaku1, Yoichi Kamagata3 and Ryuichiro Kurane3

1Kankyo Engineering Corporation, 1 Kimitsu, Kimitsu-shi, Chiba 299-1141, Japan, 2Department of Biomolecular Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan and 3National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan

We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely positioned guanine. This approach makes use of an oligonucleotide probe or primer containing a BODIPY® FL-modified cytosine at its 5'-end. When such a probe was hybridized with a target DNA, its fluorescence was quenched by the guanine in the target, complementary to the modified cytosine, and the quench rate was proportional to the amount of target DNA. This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples.

* To whom correspondence should be addressed at: National Institute of Bioscience and Human-Technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan. Tel: +81 298 61 6026; Fax: +81 298 61 6009; Email: kanagawa{at}nibh.go.jp


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