Synthesis of Photo-Responsive Acridine-Modified DNA and Its Application to Site-Selective RNA Scission

Abstract

Photo-responsive phosphoramidite monomers, which bear an azobenzene between acridine and the phosphoramidite unit, were synthesized, and incorporated into oligonucleotides. Upon UV irradiation, the azobenzene in the modified DNA efficiently isomerized from the trans isomer into the cis isomer. Although the T(m) values of their duplexes with complementary DNA were not much changed by the isomerization, site-selective RNA scission was significantly accelerated by the UV irradiation when Mn(II) ion was used as the catalyst for RNA scission.

Sulfur-Mediated Decarboxylative Coupling of 2-Nitrobenzyl Alcohols and Arylacetic Acids

“…6). 12 Based on the above results and previous studies, 5g,6b a possible mechanism is proposed (Scheme 5). Initially, complexation of DABCO base with elemental sulfur forms an active sulfur species 5g that then reacts with a phenylacetate anion to afford a benzyl polysulfide.…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…724 Acridine has also been tethered to azobenzene in an oligonucleotide in such a way that the oligonucleotide when bound to complementary RNA is cleaved only when the azobenzene is cis. 725 Use of a chiral linker between an azobenzene unit and the phosphate backbone resulted in digestion by phosphodiesterase I of only one diastereoisomer as might be expected. 726 A phenylene-ethynylene three-way building block has been used as a rigid linker to hold together three short DNA duplexes.…”

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

“…The synthetic route for the phosphoramidite of X 2 is described in [11]. The phosphoramidites for Y D and Y L were synthesized according to [13].…”

“…The phosphoramidite of X 3 was synthesized starting from the coupling between 2-chloro-4-nitrobenzoic acid and 4-isopropoxyaniline as described in [ 6 , 12 ]. The synthetic route for the phosphoramidite of X 2 is described in [ 11 ]. The phosphoramidites for Y D and Y L were synthesized according to [ 13 ].…”

“…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 ]. There, an azobenzene group was inserted between the acridine ring and the backbone of DNA as a linker (see X 2 in Figure 1 ).…”