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 a photo-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 dependent on the photocrosslinking rate of 3-cyanovinylcarbazole with d-threoninol (^CNV D), ^CNV K, or psoralen. The ultrafast RNA photocrosslinking induced the formation of a thermally irreversible covalent bond between pcASOs and the 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 D or ^CNV K targeted the RNAs with secondary structures. These results indicate the regulatory effect of photocrosslinker and photoirradiation energy using pcASOs on the gene expression level.

Keywords: 3-cyanovinylcarbazole; antisense probes; crosslinking; gene expression; ultrafast RNA photocrosslinking.