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5-(Pyren-1-yl)uracil as a Base-Discriminating Fluorescent Nucleobase in Pyrrolidinyl Peptide Nucleic Acids

Authors

  • Chalothorn Boonlua,

    1. Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330 (Thailand), Fax: (+662) 2187598
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  • Chotima Vilaivan,

    1. Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330 (Thailand), Fax: (+662) 2187598
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  • Prof. Dr. Hans-Achim Wagenknecht,

    Corresponding author
    1. Institute for Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe (Germany), Old address: Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg (Germany), Fax: (+662) 2187598
    • Hans-Achim Wagenknecht, Institute for Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe (Germany), Old address: Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg (Germany), Fax: (+662) 2187598

      Tirayut Vilaivan, Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330 (Thailand), Fax: (+662) 2187598

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  • Dr. Tirayut Vilaivan

    Corresponding author
    1. Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330 (Thailand), Fax: (+662) 2187598
    • Hans-Achim Wagenknecht, Institute for Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe (Germany), Old address: Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg (Germany), Fax: (+662) 2187598

      Tirayut Vilaivan, Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330 (Thailand), Fax: (+662) 2187598

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Abstract

A pyrene-labeled uridine (UPy) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The UPy base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (Tm) experiments. The fluorescence of the UPy-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7–41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between UPy and dA, making the UPy-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.

Abstract

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