Efficient synthesis of double dye-labeled oligodeoxyribonucleotide probes and their application in a real time PCR assay

Nucleic Acids Res. 1998 Feb 15;26(4):1026-31. doi: 10.1093/nar/26.4.1026.


A fast cleaving non-nucleosidic tetramethylrhodamine dye-labeled support has been developed for automated synthesis of double dye-labeled oligodeoxyribonucleotides in high yield. A mixture (1:1:2) of t-butylamine:methanol:water is used for cleavage and deprotection of dye-labeled oligodeoxyribonucleotides without any degradation or modification of dyes and nucleobases. The cleavage rate of oligodeoxyribonucleotides is significantly increased by using a diglycolate ester linkage instead of the commonly used succinate linkage. These double dye-labeled probes are used in PCR for real time detection of a specific PCR product. Using a 5'-exonuclease assay, detected on the ABI PRISM 7700 Sequence Detection System, there was no distinguishable difference in performance of probes synthesized using the dye-labeled support compared with traditional post-synthetic attachment of rhodamine.

Publication types

  • Comparative Study

MeSH terms

  • Base Sequence
  • Coloring Agents
  • Evaluation Studies as Topic
  • Magnetic Resonance Spectroscopy
  • Molecular Structure
  • Oligonucleotide Probes / chemical synthesis*
  • Oligonucleotide Probes / chemistry
  • Oligonucleotide Probes / genetics
  • Polymerase Chain Reaction / methods*
  • Rhodamines


  • Coloring Agents
  • Oligonucleotide Probes
  • Rhodamines
  • tetramethylrhodamine