Photoswitching of Site-Selective RNA Scission by Sequential Incorporation of Azobenzene and Acridine Residues in a DNA Oligomer

Akinori Kuzuya,Makoto Komiyama,Keita Tanaka

doi:10.4061/2011/162452

Akinori Kuzuya, Makoto Komiyama + Show 1 more

Open Access

https://doi.org/10.4061/2011/162452

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Abstract

Photoresponsive systems for site-selective RNA scission have been prepared by combining Lu(III) ions with acridine/azobenzene dual-modified DNA. The modified DNA forms a heteroduplex with substrate RNA, and the target phosphodiester linkages in front of the acridine residue is selectively activated so that Lu(III) ion rapidly cleaves the linkage. Azobenzene residue introduced adjacent to the acridine residue acts as a photoresponsive switch, which triggers the site-selective scission upon UV irradiation. A trans isomer of azobenzene efficiently suppresses the scission, whereas the cis isomer formed by UV irradiation hardly affects the scission. As a result, 1.7–2.4-fold acceleration of the cleavage was achieved simply by irradiating UV for 3 min to the mixture prior to the reaction. Considering the yield of photoisomerization, the intrinsic activity of a cis isomer is up to 14.5-fold higher than that of the trans isomer.

Highlights

In this couple of decades, significant attention has been focused on site-selective RNA scission, since it is indispensable for future molecular biology and therapy [1,2,3]
Azobenzene residue introduced adjacent to the acridine residue acts as a photoresponsive switch, which triggers the site-selective scission upon UV irradiation
Either of the 5 - or 3 -phosphodiester linkage of the target nucleotide in front of the acridine moiety, which is in protonated form under neutral condition, is site-selectively activated through general acid catalysis [6]

Summary

Introduction

In this couple of decades, significant attention has been focused on site-selective RNA scission, since it is indispensable for future molecular biology and therapy [1,2,3]. Sequence of the target site can be freely chosen, and the reaction is selective and efficient enough to achieve simultaneous tandem scission in close proximity as small as 10 nucleotides [7]. We have reported the first photoresponsive system of site-selective RNA scission by using acridine-modified DNA and free Mn(II) ion as a cleaving catalyst [11]. New photocontrollable site-selective RNA activator has been prepared by introducing an independent azobenzene residue to DNA oligomer in combination with an acridine residue (Figure 1). Such azobenzene residues in trans form stack on the acridine in the adjacent residue and efficiently inhibit the site-selective RNA activation. Clear-cut photo-control of efficient site-selective RNA scission has been successfully accomplished

Materials and Methods

12 Activator

C X3YL GATCCAGT C YL X3 GATCCAGT C X3YD GATCCAGT C YDX3 GATCCAGT C X3 GATCCAGT

Results and Discussion

Conclusions