Strong Inhibitory Effects of Antisense Probes on Gene Expression through Ultrafast RNA Photocrosslinking

Abstract

We have reported the photochemical regulation of the intracellular antisense effect of antisense probes containing ap hoto-responsive artificial nucleic acid, 3-cyanovinylcarbazole nucleoside ( CNV K). Here we focus on the importance of the photocrosslinking rate on the inhibitory effect on gene expression using photocrosslinkable antisense probes (pcASOs). The inhibitory effect of pcASOs on GFP gene expression was dependento nt he photocrosslinking rate of 3-cyanovinylcarbazole with d-threoninol ( CNV D), CNV K, or psoralen. The ultrafast RNA photocrosslinking induced the formation of at hermally irreversible covalent bond between pcASOs andt he target RNA. These ASOs strongly inhibited gene expression only when the photocrosslinking rate was faster than the random walk of branch migration. In addition, pcASOs containing CNV Do r CNV Kt argeted the RNAs with secondary structures.T hese results indicatet he regulatory effect of photocrosslinker and photoirradiation energy using pcASOs on the gene expression level.[a] Prof.

Photochemical RNA Editing of C to U by Using Ultrafast Reversible RNA Photo‐crosslinking in DNA/RNA Duplexes

“…This is possible using oligodeoxynucleotides (ODNs) that contain the ultrafast photo‐crosslinker 3‐cyanovinylcarbazole( CNV K) and pyrimidine bases in complementary DNA or RNA by photoirradiation for a few seconds, [16,17] which can be induced by irradiating at 312 nm. We demonstrate photo‐induced effects on the antisense strand using ultrafast photo‐crosslinking and generation of a duplex‐duplex invasion DNA structure; [18] therefore, photochemical C to U editing can be used in intracellular research. RNA editing may be performed by photo‐crosslinking (Figure 1).…”

Photochemical modifications for DNA/RNA oligonucleotides

“…However, these photo-crosslinkers can only crosslink to the counter base if it is adjacent to the 5 0 -side (À1) position to the crosslinker-containing base (5 0 -nXn-3 0 and 5 0 -Ynn-3 0 where X is the crosslinker-containing base and Y indicates the position of the crosslinked pyrimidine). 8,14,[106][107][108][109][110][111][112] Fujimoto et al reported that the rate constant of the photocrosslinking reaction of CNV D is 0.106 s À1 which is comparable to CNV K (0.059 s À1 ). Within the same sequence, psoralen showed a much slower photo-crosslinking rate (0.003 s À1 ) using the same wavelength (365 nm).…”

Photoinduced aggregation of liposome modified with DNA containing ultrafast DNA photo‐cross‐linker

“…1(a),(b)]. The results obtained using intracellular antisense nucleic acids 19 and the fluorescence in situ hybridization (FISH) method 20 have proven that the photochemical manipulation of DNA or RNA can be performed at the nanoscopic scale even in cells, which are more complicated systems. We also investigated DNA nanotechnology and succeeded in changing liposome membrane structures using DNA tiles by aggregation negative charges resulting from the DNA aggregation at the liposome surface.…”