Development of novel PRODAN-labeled nucleosides as base-discriminating fluorescent probes

Nucleic Acids Symp Ser (Oxf). 2006:(50):133-4. doi: 10.1093/nass/nrl066.

Abstract

We have developed a PRODAN-labeled uridine ((PDN)U), which contains a polarity-sensitive chromophore at the C-5 position of uracil. This paper describes the synthesis and fluorescent properties of oligodeoxy-nucleotides (ODNs) containing PRODAN-labeled nucleosides ((PDN)C, (PDN)A, and (PDN)G). PRODAN chromophore was attached to cytosine at the C-5 position and to purine bases at the C-8 position to extend into the major groove. When BDF probes containing a PRODAN-labeled nucleoside hybridize with a "full-matched" ODN, the fluorescence spectrum showed a strong emission around 520 nm on 450 nm excitation. In contrast, when PRODAN-labeled nucleoside analogs form a "mismatched" base pair, the fluorescence was weaker.

MeSH terms

  • 2-Naphthylamine / analogs & derivatives*
  • 2-Naphthylamine / chemical synthesis
  • 2-Naphthylamine / chemistry
  • Fluorescent Dyes / chemical synthesis
  • Fluorescent Dyes / chemistry*
  • Oligonucleotide Probes / chemistry*
  • Polymorphism, Single Nucleotide
  • Purine Nucleosides / chemical synthesis
  • Purine Nucleosides / chemistry*
  • Pyrimidine Nucleosides / chemical synthesis
  • Pyrimidine Nucleosides / chemistry*
  • Spectrometry, Fluorescence

Substances

  • Fluorescent Dyes
  • Oligonucleotide Probes
  • Purine Nucleosides
  • Pyrimidine Nucleosides
  • 2-Naphthylamine