RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes

Bioorg Med Chem Lett. 2016 Nov 1;26(21):5312-5314. doi: 10.1016/j.bmcl.2016.09.035. Epub 2016 Sep 15.


Photo-cross-linkable fluorescent oligodeoxyribonucleotides having 3-cyanovinylcarbazole nucleoside were applied to fluorescence in situ hybridization (FISH) based 16S rRNA detection in Escherichia coli cells. As the photo-cross-linked probe/rRNA hybrid was stable under the denaturing condition, decrease of the fluorescence signal through the washing process was prevented. The thermally irreversible hybridization property also enabled stable hybridization with the structured region on the target RNA, and facilitated design of the sequence for the FISH probe. Further development of the method might contribute to quantitative and stable FISH staining.

Keywords: 16S rRNA; 3-Cyanovinylcarbazole nucleoside; Fluorescence in situ hybridization; Photo-cross-link.

MeSH terms

  • Carbazoles / chemistry*
  • Escherichia coli / genetics
  • In Situ Hybridization, Fluorescence / methods*
  • Molecular Probes
  • Oligodeoxyribonucleotides / chemistry*
  • Photochemical Processes*
  • RNA / chemistry*


  • Carbazoles
  • Molecular Probes
  • Oligodeoxyribonucleotides
  • RNA