Frontiers and Approaches to Chemical Synthesis of Oligodeoxyribonucleotides

Abstract

The advantages and disadvantages of existing approaches to the synthesis of oligodeoxyribonucleotides (ODN) are discussed focusing on large-scale methods. The liquid phase and solid supported synthesis and the synthesis on soluble polymers are discussed. Different problems concerning the methods and implementation of the ODN synthesis are outlined depending on goals of using target oligomers.

Non-coding RNAs as drug targets

“…Landmark achievements in the therapeutic development of oligonucleotides have included 1) the ability to synthesize kilogram quantities of oligonucleotide at costs that are compatible with clinical application 14 , 2) the demonstration that chemical modifications can reduce off-target effects (see below), lower toxicity, and improve pharmacokinetic properties 7,15 , 3) the demonstration that synthetic nucleic acids can be administered systemically and knock down their intended targets in vivo 7,15 ; and 4) the FDA approval of two synthetic oligonucleotides designed to target mRNA and numerous ongoing trials 16-18 .…”

Solution‐Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials

“…[28][29][30] Although branched intermediates with DNA chains linked to soluble supports have been reported, the largest products of such syntheses reported in the recent literature contain no more than 5-9 nucleotides in total, [25][26][27] demonstrating how difficult it is to prepare large oligonucleotides without immobilization. [28][29][30] Although branched intermediates with DNA chains linked to soluble supports have been reported, the largest products of such syntheses reported in the recent literature contain no more than 5-9 nucleotides in total, [25][26][27] demonstrating how difficult it is to prepare large oligonucleotides without immobilization.…”

“…As a consequence, new methods for solution-phase synthesis that avoid or reduce the high cost and limited scalability of solid-phase syntheses [24] are being developed. [25][26][27] Further, there is active research on new approaches (hexamer arms) and 11 % over 25 steps (octamer arms) of HPLC-purified compounds were obtained. The adamantanebased hybrids show more DNA-dominated assembly properties than their analogues with larger lipophilic cores.…”

Polymerizable phosphoramidites with an acid-cleavable linker for eco-friendly synthetic oligodeoxynucleotide purification

“…[12][13][14][15][16] Gene synthesis requires hundreds of ODNs. Most of the challenges for large scale oligo synthesis have been overcome, 12,13 but large scale purification remains a bottleneck. Due to automated ODN synthesis either using modern column-based synthesizers or microarray technologies, large numbers of ODNs can be synthesized simultaneously.…”