Best Minimally Modified Antisense Oligonucleotides According to Cell Nuclease Activity

Abstract

Minimally modified oligonucleotides belong to the second-generation antisense class. They are phosphodiester oligonucleotides with a minimum of phosphorothioate linkages in order to be protected against serum and cellular exonucleases and endonucleases. They activate RNase H, have weak interactions with proteins, and have thus a better antisense efficiency. Two of them have been designed from an all-phosphorothioate antisense oligonucleotide directed against mdr1-expressing cells. They are protected against serum and cellular enzymatic degradation by the self-forming hairpin d(GCGAAGC) at their 39 -end and by judiciously located phosphorothioate residues, depending on the cellular composition in exonucleases or endonucleases. Besides their already demonstrated ability to cleave pyrimidine sites, endonucleases show some specificity for CpG sites. Their activity is hindered if specific sites are involved in secondary structure as hairpin.

A Promising Strategy Against SARS-CoV-2 Infected Patients: Antisense Therapy

“…Natural phosphodiester oligonucleotides are quickly digested by cellular nucleases in the cell (Djavanbakht Samani et al, 2001). Therefore, ASOs were modified to some forms that are nucleaseresistant and appropriate for research purposes ( 7c).…”

Aptamers as Theranostic Agents: Modifications, Serum Stability and Functionalisation

“…One common method has been to cap the 3′- and/or 5′- ends of the nucleic acid strand [19], which prevents attacks by exonucleases. Endonucleases, however, appear to have a preference for pyrimidines, with cleavage occurring more frequently in the case of two or more adjacent pyrimidines [20,21]. One of the first types of modification introduced to enhance the stability of ASOs was the use of phosphorothioate nucleotides as an alternative backbone.…”

“…In the case of the phosphorothioate base, one of the non-bridging phosphate oxygens in the phosphodiester linkage is substituted for sulphur [22]. This has proven to be very effective in protecting ASOs against exonucleases when placed in the 5′- or 3′- end of the oligonucleotide, with it appearing to be most effective when placed at the 3′-side of the internal pyrimidine [20]. However, it has been suggested that these are “stickier” towards proteins than the normal phosphodiester backbone [23], which may present a problem with aptamers and non-specific binding.…”

A Promising Strategy Against SARS-CoV-2 Infected Patients: Antisense Therapy

“…Liang et al, 2017). Thus, secondary structures of three viral regions on SARS-CoV-2 genomic RNA; 5`UTR, start codon, and or 3`UTR as the target in ASO design were predicted using Natural phosphodiester oligonucleotides are quickly digested by cellular nucleases in the cell (DjavanbakhtSamani et al, 2001). Therefore, ASOs were modified to some forms that are nucleaseresistant and appropriate for research purposes (Table2).…”