Synthesis and Triple‐Helix‐Stabilization Properties of Branched Oligonucleotides Carrying 8‐Aminoadenine Moieties

Abstract

The synthesis of several branched oligonucleotides, i.e., of the parallel hairpins 5 ± 8 and the Y-shaped 9 is described, together with their use in the formation of pyrimidine ¥ pyrimidine ¥ purine triple helices. Special attention was paid to the optimization of the assembly of the second strand from asymmetric branching molecules. The presence of 8-aminoadenine moieties in the WatsonÀCrick purine strand and 2'-O-methyl-RNA in the Hoogsteen pyrimidine strand produced strong stabilization of the triplex.

Synthesis, Cell-Surface Binding, and Cellular Uptake of Fluorescently Labeled Glucose−DNA Conjugates with Different Carbohydrate Presentation

“…showing that these side products lack one or two glucose residues. This confirms that phosphoramidite couplings after branching are somehow less efficient according to literature (33,34) but this fact did not prevent obtaining pure oligonucleotide conjugates with two and four glucose units. temperature.…”

Design, synthesis and evaluation of novel, branched trident small interfering RNA nanostructures for sequence-specific RNAi activity

“…Also, branched oligonucleotides have been reported to exhibit high affinity for single-strand oligonucleotides to form alternated strand triplexes. [25][26][27] However, the simultaneous synthesis of three identical arms of the RNA using a modied solid-support, to yield branched RNA structure forming a nano-assembly, remains unexplored.…”

Parallel Clamps and Polypurine Hairpins (PPRH) for Gene Silencing and Triplex‐Affinity Capture: Design, Synthesis, and Use

“…These asymmetric branching units are diol derivatives protected with fluorenyloxycarbonyl (Fmoc) and DMT groups. These derivatives allow synthesis of one of the strands elongating the DMT‐protected part, and the assembly of the second strand in the normal 3′‐5′ direction, avoiding the need of reversed 5′‐phosphoramidites (Aviñó, Grimau, Frieden, & Eritja, ). Another alternative method for the preparation of parallel clamps without the use of 5′‐phosphoramidite is preparing both polypurine and polypyrimidine strands on separate supports and then linking them using the Cu(I)‐catalyzed cycloaddition reaction (Click reaction) (Alvira & Eritja, ).…”