Fluorescence quenching of TMR by guanosine in oligonucleotides |
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| Authors: | Peng Qu XuDong Chen XiaoXue Zhou Xun Li XinSheng Zhao |
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| Institution: | 1.Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Department of Chemical Biology, College of Chemistry and Molecular Engineering,Peking University,Beijing,China |
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| Abstract: | 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. |
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