Effect of linker length on photo-cross-linking position mediated by click chemistry via [2 + 2]photocycloaddition

Abstract

Ultrafast reversible DNA/RNA photo-cross-linking is a powerful tool for regulating the target strand in living cells. In particular, 3-cyanovinylcarbazole (^CNVK) and 3-cyanovinylcarbazole modified by D-threoninol (^CNVD) can photo-cross-link to pyrimidine bases within a few seconds of photoirradiation. However, these photo-cross-linkers can only cross-link to the counter base if it is adjacent to the 5′-side (−1 position). In this study, we synthesized novel photo-cross-linkers with varying linker lengths capable of photo-cross-linking with pyrimidine bases at locations other than the −1 position via click chemistry. The photo-cross-linking site was dependent on linker length.