C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability

Abstract

Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.

Recent developments in reversible photoregulation of oligonucleotide structure and function

“…12d). 126 Unfortunately, after inclusion in an oligonucleotide, the stabilizing effect of the bridge appeared to be completely neutralized by the azobenzene inclusion. Nuclease resistance was also measured, and although 3 0 -phosphate scission proceeded at the same rate as for the native strand, 5 0 -phosphate scission relative to the LNA was 300-fold decreased.…”

Azobenzene C‐Nucleosides for Photocontrolled Hybridization of DNA at Room Temperature

“…Azobenzenes, [44,45] spiropyrans, [46] and diarylethenes [31,46] have been attached to nucleobases, whereas other approaches used the nucleobase as parto fa na rylvinyl [47][48][49] or diarylethene [30] photoswitch. In somec ases, wavelengths of l = 254 nm were necessary [49] or only moderate destabilization effects were reported [30,[44][45][46]49] -p robablyb ecause of the location of the photoswitch in the major groove. [44] Attachmentso f azobenzenes [50,51] and spiropyrans [27] to the 2'-functionality of ar ibose ring and phosphate backbone have also been reported (see reference [9] for ar eview).…”

“…Azobenzenes,44, 45 spiropyrans,46 and diarylethenes31, 46 have been attached to nucleobases, whereas other approaches used the nucleobase as part of an arylvinyl47–49 or diarylethene30 photoswitch. In some cases, wavelengths of λ =254 nm were necessary49 or only moderate destabilization effects were reported30, 44–46, 49 – probably because of the location of the photoswitch in the major groove 44.…”

Synthesis, characterization and in vitro biological screening of 4-hydroxy naphthalen-1-yl, naphtho[1,2-b]furan, benzo[h]chromene and 5,6-dihydropyridazine derivatives containing sulfonamide moiety

“…Substituted azobenzene have attracted considerable attention based on their various physical and chemical properties, such as bright colors, good stability, low flammability, and rapid, reversible photo-isomerization [1][2][3][4] . Aromatic azo compounds are widely used in the chemical industry as dyes, pigments 5,6 , food additives 7, indicators 3 , radical reaction initiators 8 and therapeutic agents 9,10 . Also, azobenzenes have shown promising applications in photo-optical media 11 , photoswitches 12 , photo-mechanical systems 13 , micro patterning 14 , nonlinear optical media 15 , molecular shuttles 16 , nanotubes 17 , and in the manufacture of protective eye glasses and filters 18 .…”