Reagents for addressed modification of biopolymers: 11. The synthesis ofN Im-2,4-dinitrophenyl derivatives of histidine and urocanic and imidazolylacetic acids for anchoring imidazole residues to oligonucleotides

Site-selective artificial ribonucleases: oligonucleotide conjugates containing multiple imidazole residues in the catalytic domain

Design of site-selective artificial ribonucleases (aRNases) is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s) of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond.

4-aminometyl-3-nitrobenzoic acid--a photocleavable linker for oligonucleotides containing combinatorial libraries

We detail the design, synthesis, and characterization of an o-nitrobenzyl-based photolabile linker containing amine and carboxyl anchor groups. A model nucleoside monomer modified with an imidazole residue and a precursor unit linked to a heterocyclic base through a photolabile tether is constructed Upon UV irradiation (313- 365 nm), the imidazole containing part of this molecule is released.