Synthesis and purification of biotinylated oligodeoxynucleotides containing single TpT dimeric pyrimidine (6-4) pyrimidone lesion

  • Danni Wu
  • Ning Zhang
  • Bingjie Kong
  • Haiying Hang
  • Hailin WangEmail author
Research Paper
Part of the following topical collections:
  1. New Insights into Analytical Science in China


Ultraviolet (UV) radiation could induce pyrimidine-related dimeric lesions in genomic DNA. Though the cyclobutane pyrimidine dimers (CPDs) are the most abundant UV-induced lesions, the pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) may have more serious, potentially lethal, and mutagenic effects. It is important to have 6-4PP-containing oligodeoxynucleotides to be prepared for studying their adverse biological effects. Here, we developed a UV-irradiated water droplet method for the preparation of a biotinylated, 6-4PP-containing 10-mer oligodeoxynucleotide. By the use of HPLC purification and enrichment twice, the final yield is estimated to be about 8.1%. In contrast, without applying droplet technique, the direct UV irradiation against oligonucleotide-containing aqueous solution, the product yield is very low. The enzymatic hydrolyzation of the obtained product shows a 6-4PP characteristic ion transition of 545.12 → 432.13 in negative ion mode UHPLC-Q-TOF/MS. The established procedure for the preparation of 6-4PP-containing oligonucleotides is convenient with an improved yield.

Graphical abstract


UV irradiation Pyrimidine (6-4) pyrimidone (6-4PP) HPLC UHPLC-Q-TOF/MS 


Funding information

This work is supported by the National Natural Science Foundation of China (21435008, 9174321, and 21527901), Sanming Project of Medicine in Shenzhen (SZsm201811070), the Key Research Program of Frontier Sciences, CAS (QYZDJ-SSW-DQC017), and the K.C. Wong Education Foundation.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Danni Wu
    • 1
  • Ning Zhang
    • 1
  • Bingjie Kong
    • 2
  • Haiying Hang
    • 2
  • Hailin Wang
    • 1
    • 3
    Email author
  1. 1.State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental SciencesChinese Academy of SciencesBeijingChina
  2. 2.Key Laboratory for Protein and Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of BiophysicsChinese Academy of SciencesBeijingChina
  3. 3.University of Chinese Academy of SciencesBeijingChina

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