Design and synthesis of new acid cleavable linkers for DNA sequencing by synthesis

  • Nucleosides Nucleotides Nucleic Acids. 2014;33(12):774-85. doi: 10.1080/15257770.2014.945647.
Min Jiang  1 ,  Daonian Tang ,  Xiaodong Zhao ,  Qing Li ,  Yuan Zhuang ,  Xiaofei Wei ,  Xiaowei Li ,  Yazhi Liu ,  Xin-Yan Wu ,  Zhifeng Shao ,  Bing Gong ,  Yu-Mei Shen
Affiliations
  • 1. a Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine and Bio-ID Center , Shanghai Jiao Tong University , Shanghai , China.
PMID: 25372993 DOI: 10.1080/15257770.2014.945647
Abstract

A new kind of acid sensitive tetrahydrofuranyl (THF) linker was synthesized and then reacted with 5-(6)-carboxytetramethylrhodaminesuccinimidyl ester (5(6)-TAMRA, SE), followed by di(N-succinimidyl) carbonate (DSC) and modified 2'-deoxyuridine triphosphate (dUTP); the final product, as a reversible terminator for DNA Sequencing by synthesis (DNA SBS), was given obtained and confirmed by 1H-NMR, 31P-NMR, and HRMS with purity of up to 99%. The synthesized dye-labeled terminator incorporated into DNA strand successfully, and the fluorophore was cleaved completely under acidic conditions. The preliminary results encourage us to explore more acid-sensitive linkers for DNA SBS to increase the cleavage efficiency under weakly acidic conditions.

Keywords
Triphosphate analogues; fluorescent base analogues; synthetic methodology.
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