RNA fluorescence in situ hybridization hybridisation using photo-cross-linkable beacon probes containing pyranocarbazole in living E. coli

Crosslinker-modified nucleic acid probes for improved target identification and biomarker detection

“…This methodology is commonly employed for investigating the location of nucleic acids in cells. 61,62 In the here described application, a molecular beacon modified at the 5′ end with a fluorophore ( e.g. Cy3) and at the 3′ end with a quencher ( e.g.…”

Fluorescence In Situ Hybridization of 16S rRNA in Escherichia coli Using Multiple Photo‐Cross‐Linkable Probes

“…We have previously reported on RNA FISH using an ultrafast photo-cross-linking reaction. [28,29] In the ultrafast photo-cross-linking, DNA/RNA inter-strand cross-linking can be achieved by irradiating the double strand of DNA and target RNA containing photoresponsive artificial nucleic acid such as 3-cyanovinylcarbazole ( CNV K) [30,31] or pyranocarbazole ( pc X). [32] RNA FISH using a photo-cross-linkable probe can be washed with a buffer containing a denaturant and detected at a very high signal to noise (S/N) ratio because a photo-cross-linkable FISH probe containing CNV K or PC X can bind to the target RNA.…”

“…The development of technology to detect these various higher‐order structures with high sensitivity is a challenge for the RNA‐FISH method for diagnosis. We have previously reported on RNA FISH using an ultrafast photo‐cross‐linking reaction [28,29] . In the ultrafast photo‐cross‐linking, DNA/RNA inter‐strand cross‐linking can be achieved by irradiating the double strand of DNA and target RNA containing photoresponsive artificial nucleic acid such as 3‐cyanovinylcarbazole ( CNV K) [30,31] or pyranocarbazole ( pc X) [32] .…”

DNA photo-cross-linking using a pyranocarbazole-modified oligodeoxynucleotide with a d-threoninol linker

“…We report pyranocarbazole ( PC X) as a photo-cross-linker that can photo-crosslink to pyrimidine in complementary DNA or RNA strand under visible light. 11 It was anticipated that his photo-cross-linker would accelerate the intracellular application of nucleic acid photo-cross-linking such as photochemical regulation of gene expression 12 and detection of RNA strand; 13 however, photocross-linking using PC X to cytosine requires photoirradiation for 1 min, and it is necessary to speed up this process. Besides, the ribose backbone, D-threoninol backbone, 14 and serinol backbone 15 have been reported as the backbone of the articial nucleic acid.…”

“…3H, J ¼ 7.2 Hz) 13. C NMR (100 MHz, CDCl 3 ) 167.8, 161.6, 153.5, 144.6, 143.1, 141.7, 126.9, 122.7, 121.1, 121.0, 120.6, 119.7, 112.9, 112.7, 108.9, 96.1, 62.2, 45.0, 14.3.…”