A Versatile Solid-Phase Approach to the Synthesis of Oligonucleotide Conjugates with Biodegradable Hydrazone Linker

One of the ways to efficiently deliver various drugs, including therapeutic nucleic acids, into the cells is conjugating them with different transport ligands via labile or stable bonds. A convenient solid-phase approach for the synthesis of 5′-conjugates of oligonucleotides with biodegradable pH-sensitive hydrazone covalent bonds is proposed in this article. The approach relies on introducing a hydrazide of the ligand under aqueous/organic media to a fully protected support-bound oligonucleotide containing aldehyde function at the 5′-end. We demonstrated the proof-of-principle of this approach by synthesizing 5′-lipophilic (e.g., cholesterol and α-tocopherol) conjugates of modified siRNA and non-coding RNAs imported into mitochondria (antireplicative RNAs and guide RNAs for Mito-CRISPR/system). The developed method has the potential to be extended for the synthesis of pH-sensitive conjugates of oligonucleotides of different types (ribo-, deoxyribo-, 2′-O-methylribo-, and others) with ligands of different nature.     

Suppression of MDR1 gene expression by chemically modified siRNAs

The ability of chemically modified siRNAs targeted to MDR1 mRNA to inhibit P-glycoprotein expression and to restore sensitivity of cancer cells to antibiotic vinblastine was investigated. The effects of chemical modifications on RNA stability in cell culture medium and inhibition of MDR1 gene expression were tested. We found that siRNAs containing 2′-O-methyl ribonucleotides within either sense or/and antisense strands display high stability in serum but exhibit a significant reduction in the biological activity. The protection of 3′-ends of siRNA by introduction of 3′-3′-inverted phosphodiester bonds and two 2′-O-methyl ribonucleotides in protruding 3′-ends considerably increase their biological activity, which allows a 30-fold decrease in the cytostatic agent concentration required for cancer cell death. The data obtained demonstrate that the chemically modified siRNAs can be considered as potential therapeutics, which enhances the efficiency of cancer chemotherapy. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1227–1235, July, 2006.     

Nonenzymatic recombination of RNA by means of transesterification

Coupled nonenzymatic cleavage/ligation of oligoribonucleotides catalyzed by magnesium ions afforded longer RNA molecules with a new sequence. The efficiency of formation of ligation products reaches 6%. The possible role of this reaction in the evolution of the RNA world is discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2413–2419, December, 2007.     

Site-directed cleavage of DNA by an oligonucleotide conjugate with o-bromobenzoic acid in the presence of copper ions

Site-directed cleavage of single- and double-stranded DNAs by an oligonucleotide conjugate with 5-[N-(3-aminopropyl)sulfamoyl]-2-bromobenzoic acid was investigated. When forming duplex complexes with a single-stranded DNA and triplex complexes with a double-stranded DNA, this conjugate cleaves DNA near the binding site in the presence of copper ions and free o-bromobenzoic acid. The efficacy and specificity of DNA cleavage by this conjugate and other oligonucleotide conjugates bearing tetracarboxyphthalocyanine Co^II and bleomycin A5 as reactive groups were compared.     

Reversion of the multiple-drug resistance phenotype mediated by short interfering RNAs

Repression of MDR1 gene expression and restoration of cancer cell sensitivity to cytostatic agents were studied with the use of synthetic siRNAs directed to different MDR1 mRNA regions. Short interfering RNAs that enhance sensitivity of drug-resistant cells to vinblastine were revealed. The ability of various siRNAs to repress gene expression does not correlate with the efficiency of antisense oligonucleotides complementary to the same mRNA regions. An siRNA sample remained intact in a medium during a period of time sufficient to exhibit biological activity. The results of our study suggest that siRNAs can be considered as a basis for therapeutic drugs for enhancement of the efficiency of antitumor chemotherapy. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1260–1267, May, 2005.