Fluorescence quenching of TMR by guanosine in oligonucleotides

Peng Qu, Xudong Chen, Xiaoxue Zhou, Xun Li, Xinsheng Zhao

Research output: Contribution to journalArticlepeer-review


Nucleotide-specific fluorescence quenching in fluorescently labeled DNA has many applications in biotechnology. We have studied the inter- and intra-molecular quenching of tetramethylrhodamine (TMR) by nucleotides to better understand their quenching mechanism and influencing factors. In agreement with previous work, dGMP can effectively quench TMR, while the quenching of TMR by other nucleotides is negligible. The Stern-Volmer plot between TMR and dGMP delivers a bimolecular quenching constant of K s = 52.3 M -1. The fluorescence of TMR in labeled oligonucleotides decreases efficiently through photoinduced electron transfer by guanosine. The quenching rate constant between TMR and guanosine was measured using fluorescence correlation spectroscopy (FCS). In addition, our data show that the steric hindrance by bases around guanosine has significant effect on the G-quenching. The availability of these data should be useful in designing fluorescent oligonucleotides and understanding the G-quenching process.

Original languageEnglish (US)
Pages (from-to)1653-1659
Number of pages7
JournalScience in China, Series B: Chemistry
Issue number10
StatePublished - Oct 2009


  • FCS
  • Fluorescence
  • G-quenching
  • Guanosine
  • Oligonucleotides
  • PET
  • TMR

ASJC Scopus subject areas

  • General Chemistry


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