Triazinylamidophosphate Oligonucleotides: Synthesis and Study of Their Interaction with Cells and DNA-Binding Proteins

Influence of Combinations of Lipophilic and Phosphate Backbone Modifications on Cellular Uptake of Modified Oligonucleotides

“…The analysis of the flow cytometry data showed that the other studied factors besides the number of DMI groups ( Figure 4 ) are able to remarkably influence the accumulation efficiency of the investigated lipophilic phosphate-modified oligonucleotides. Dodecyl- and cholesterol-containing conjugates ( Figure 4 b, oligonucleotides A, B, and H) have an increased cellular uptake, as shown previously [ 34 , 36 , 37 , 58 ]. The contribution of not only the different nature of the lipophilic part (A vs. H) but also of the nucleotide sequence (A vs. B) to the delivery efficiency was observed with fluorescence signal differences up to several times ( Figure 4 b).…”

“…For quantitative assessment of the efficiency of intracellular accumulation of oligonucleotides with different numbers of DMI groups, transfection was carried out for 4 h in a serum-free DMEM medium with a 1 or 5 μM concentration of oligonucleotides in the HEK293T cell line, which has been proved to be a convenient model to study the cellular uptake of NA derivatives [ 34 , 36 , 37 , 64 , 65 ]. The transfected cells were analyzed using flow cytometry ( Figure 2 ).…”

“…The insertion of triazinyl phosphoramidate (TPA) modification bearing two dodecyl residues in appropriate oligonucleotide structures using a triazine modifier during the modified protocol of the oxidation step was performed as described in [ 34 ].…”

“…Over the past decade, several chemical approaches utilizing alternative oxidation steps to obtain novel structures of modified phosphate groups, which allow one not only to change the nature of the phosphate backbone but also to apply the chemistry of its introduction to varying desirable functional moieties, have been proposed [ 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. In particular, we have adopted the method of using electron-deficient azides in the Staudinger reaction during the oxidation step to efficiently obtain various phosphate derivatives [ 34 , 35 , 36 , 37 , 38 , 39 ]. We have also demonstrated that different representatives of the developed phosphoryl guanidine and triazinyl phosphoramidate modifications can be applied for the synthesis of lipophilic oligonucleotides with enhanced levels of intracellular accumulation [ 37 ].…”

Self-Penetrating Oligonucleotide Derivatives: Features of Self-Assembly and Interactions with Serum and Intracellular Proteins

“…Oligonucleotide derivatives containing three dodecyl residues in the non-nucleotide unit are also able to efficiently penetrate cells in vitro in the absence of transfection agents and form stable complexes with albumin under electrophoretic conditions [ 65 , 66 ]. This work reports on self-assembly and non-covalent interactions with human serum albumin (HSA) of amphiphilic triazinyl phosphoramidate oligonucleotide derivatives, functionalized with two dodecyl groups [ 67 ]. The derivatives were studied for their ability to form micelle-like structures and to associate with HSA.…”