BODIPY fluorophores for nucleic acid labelling

BODIPY fluorophores for nucleic acid labelling

Project No. 2024

Principal Investigator/Inventor: Dr. Hongbin (Tony) Yan, Department of Chemistry

Compounds and methods for labeling DNA and RNA oligonucleotides with BODIPY fluorphores during solid phase oligonucleotide synthesis.

Compared with other fluorophores for nucleic acid labelling, BODIPYs are generally more photostable, and their fluorescence is pH-independent making them well suited for applications such as sequencing. Dr. Yan and his lab have developed a method for the direct incorporation of BODIPY into nucleic acids during solid phase synthesis. Until now, BODIPY fluorophore use has been limited to post-synthetic conjugation. Normally, BODIPY is not stable under the conditions for solid phase nucleic acid synthesis however, the research team has identified the causes for this instability and invented stable BODIPY analogues that are compatible with these synthetic conditions so it is now possible for the phosphoramidite chemistry to be implemented. This process streamlines the nucleic acid labelling process and eliminates the need for tedious post-synthetic handling. This process can be implemented into commercial DNA synthesizers to produce highly fluorescent oligonucleotides.

Patent Status

Yan and Tram. “Compounds for fluorescent labeling” US patent application 13/239,705, Sep. 22, 2011.


Yang, L. et al., (2011) Some observations relating to the stability of the BODIPY fluorophore under acidic and basic conditions, Dyes and Pigments. 91: 264-267.
Tram, K. et al., (2011) Oligonucleotide labeling using BODIPY phosphoramidite, Nucleoside, Nucleotides & Nucleic Acids. 30: 1-11.


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