Photoregulating RNA Digestion Using Azobenzene Linked Dumbbell Antisense Oligodeoxynucleotides

Abstract

Introduction of 4,4'-bis(hydroxymethyl)-azobenzene (azo) to dumbbell hairpin oligonucleotides at the loop position was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation. Here, we designed and synthesized a series of azobenzene linked dumbbell antisense oligodeoxynucleotides (asODNs) containing two terminal hairpins that are composed of an asODN and a short inhibitory sense strand. Thermal melting studies of these azobenzene linked dumbbell asODNs indicated that efficient trans to cis photoisomerization of azobenzene moieties induced large difference in thermal stability (ΔTm = 12.1-21.3 °C). In addition, photomodulation of their RNA binding abilities and RNA digestion by RNase H was investigated. The trans-azobenzene linked asODNs with the optimized base pairs between asODN strands and inhibitory sense strands could only bind few percentage of the target RNA, while it was able to recover their binding to the target RNA and degrade it by RNase H after light irradiation. Upon optimization, it is promising to use these azobenzene linked asODNs for reversible spatial and temporal regulation of antisense activities based on both steric binding and RNA digestion by RNase H.

Recent developments in reversible photoregulation of oligonucleotide structure and function

“…In the current example, either the deactivated dumbbell has a relatively high cleavage rate (19.9%, with 83.5% for the activated dumbbell) or, for a different sequence, the activated dumbbell has a low cleavage rate (36.7%, with 4.9% for the deactivated dumbbell). Therefore, the current system 142 does not improve much on the photoregulated oligonucleotide cleavage reported by Zou, Yang and co-workers. 94…”

“…18). 142 The dumbbells are formed from a binding site linked to two short complementary strands via two linkers 10. Under ambient conditions, the linkers are in the trans configuration and hairpin structure is stabilised.…”

Controlling Gene‐Silencing with Azobenzene‐Containing siRNAs (siRNAzos)

“…Asunama and his group made DNA molecules that were photo‐switchable by attaching an azobenzene monomer to d ‐threinol in order to control duplex formation in real time (Kashida, Fujii, & Asanuma, 2008). In addition, within the last 5 years, there have been advances in controlling RNA/DNA hybridization with azobenzene (Goldau, Murayama, Brieke, Asanuma, et al., 2015; Goldau, Murayama, Brieke, Steinwand, et al., 2015), as well as azobenzene‐mediated control of RNase H activity in real time with various light sources (Wu, He, & Tang, 2015). This short summary highlights how useful and versatile azobenzene is.…”

Reversible photoregulation in biological systems via introduction of azobenzene into nucleic acid

“…然而Yamana 等 [88] 曾将酰胺键引入发夹核酸骨架位置上, 但偶氮苯 的异构化作用没有能够开启核酸的结构. Schatz和Mir-kin等 [89] 加7.5倍 [90] . 这个结果与杨等 [91] 曾报道的使用3个偶氮 苯替代单元设计的DNA纳米剪进行DNA断裂的结果 相当.…”