Phthalimide–Oxy Derivatives for 3′‐ or 5′‐Conjugation of Oligonucleotides by Oxime Ligation and Circularization of DNA by “Bis‐ or Tris‐Click” Oxime Ligation

Abstract

A solid support and two phosphoramidites exhibiting a phthalimide–oxy group were synthesized. First, after treatment with hydrazine, the resulting 5′‐ and 3′‐oxyamine oligonucleotides were conjugated with aldehyde derivatives by oxime ligation. Second, oligonucleotides exhibiting an oxyamine at each end were circularized by means of different dialdehydes. Cyclic oligonucleotides of different lengths (9 to 31‐mer) were rapidly obtained without the need of a template. Finally, a bicyclic oligonucleotide was synthesized starting form an oligonucleotide bearing three oxyamines, which reacted with a trialdehyde to form three oxime ligations.

Fine-tuning the properties of the thrombin binding aptamer through cyclization: Effect of the 5′-3′ connecting linker on the aptamer stability and anticoagulant activity

“…In particular, cycTBA I and II were obtained using a chemical cyclization strategy based on the oxime ligation method, [46,47] while cycTBA III and IV were circularized using a Cu(I)-assisted azide-alkyne cycloaddition (CuAAC) protocol, [48] also adopted to obtain our first prototype, cycTBA. [42] More in detail, cycTBA I was prepared also to evaluate whether the oxime ligation approach was more efficient, in terms of cyclization yields, than the alternative, previously explored CuAAC.…”

“…terminal 2′-deoxyguanosines of the TBA sequence (Table 1) -were successfully synthesized and characterized. The cyclic TBAs indicated as cycTBA I and cycTBA II, with a 22-and 30-atom linker, were respectively prepared by using oxime [46] and bis-oxime [47] ligation procedure; while cycTBA III and cycTBA IV, with a 34-and 48-atom linker, respectively, were obtained by CuAAC. [42,48] cycTBA I was synthesized according to the strategy developed by Dumy et al [46], exploiting the oxime ligation between an oxyamine linker introduced at the 5′-end and an aldehyde function generated by oxidation of a 3′-glycerol moiety (Scheme 2).…”

Solid Supports for the Synthesis of 3′-Aminooxy Deoxy- or Ribo-oligonucleotides and Their 3′-Conjugation by Oxime Ligation

“…[22][23][24][25][26][27][28][29][30] With regards to oxime ligation, several phosphoramidite derivatives have been reported for the introduction of the aminooxy function at the 5'-end of oligonucleotides for their subsequent conjugation or cyclization. [23][24][25][31][32][33][34][35] In contrast, the 3'-conjugation of oligonucleotides by oxime ligation has been poorly explored. The usual method reported in the literature to do so is to introduce a glycerol group at the 3'-end which is further oxidize to an aldehyde to eventually reacts with a aminooxy derivative.…”

“…Only one recent publication, from our group, reported the synthesis of a solid support allowing for the introduction of the aminooxy function at the 3'-end of oligonucleotides (Figure 1). 35 The resulting 3'-modified oligonucleotides were then conjugated with different aldehyde derivatives or circularized by means of bis-oxime ligation after the introduction of another aminooxy function at the 5'-end and reaction with a dialdehyde. 35…”

“…35 The resulting 3'-modified oligonucleotides were then conjugated with different aldehyde derivatives or circularized by means of bis-oxime ligation after the introduction of another aminooxy function at the 5'-end and reaction with a dialdehyde. 35…”