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Fluorescence quenching of TMR by guanosine in oligonucleotides

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Abstract

Nucleotide-specific fluorescence quenching in fluorescently labeled DNA has many applications in biotechnology. We have studied the inter- and intra-molecular quenching of tetramethylrhodamine (TMR) by nucleotides to better understand their quenching mechanism and influencing factors. In agreement with previous work, dGMP can effectively quench TMR, while the quenching of TMR by other nucleotides is negligible. The Stern-Volmer plot between TMR and dGMP delivers a bimolecular quenching constant of K s = 52.3 M−1. The fluorescence of TMR in labeled oligonucleotides decreases efficiently through photoinduced electron transfer by guanosine. The quenching rate constant between TMR and guanosine was measured using fluorescence correlation spectroscopy (FCS). In addition, our data show that the steric hindrance by bases around guanosine has significant effect on the G-quenching. The availability of these data should be useful in designing fluorescent oligonucleotides and understanding the G-quenching process.

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Authors and Affiliations

  1. Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China

    Peng Qu, XuDong Chen, XiaoXue Zhou, Xun Li & XinSheng Zhao

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  1. Peng Qu
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  2. XuDong Chen
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  3. XiaoXue Zhou
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  4. Xun Li
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  5. XinSheng Zhao
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Correspondence to XinSheng Zhao.

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Supported by the National Natural Science Foundation of China (Grant Nos. 20673002, 20733001) and the 973 Project (2006CB910304)

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Qu, P., Chen, X., Zhou, X. et al. Fluorescence quenching of TMR by guanosine in oligonucleotides. Sci. China Ser. B-Chem. 52, 1653–1659 (2009). https://doi.org/10.1007/s11426-009-0235-4

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  • DOI: https://doi.org/10.1007/s11426-009-0235-4

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