Synthetic Errors During Solid-Phase Phosphoramidite Synthesis of Oligonucleotides
- 1Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk 630090, Russia
Abstract
While solid-phase phosphoramidite chemistry remains the gold standard for nucleic acid synthesis, the rigorous purity requirements of modern therapeutic oligonucleotides demand a much tighter control over side reactions. This review critically examines the underlying mechanisms of impurity formation during chain assembly and evaluates practical strategies to mitigate them. We detail key nucleobase degradation pathways, specifically O6-guanine phosphitylation, acrylonitrile-induced alkylation, cytidine deamination, and acid-catalyzed adenine depurination. Furthermore, we address current debates surrounding the capping step, contrasting the sequence errors induced by traditional anhydride-based mixtures with the protective benefits of phosphoramidite-based capping reagents. By mapping these chemical trade-offs and evaluating various protecting group strategies, we emphasize the growing need to shift from universal synthetic cycles toward context-dependent protocols, tailoring reaction conditions to specific sequences to ensure maximum fidelity.
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BibTeX
@article{sherstyuk2026synthetic,
title = {{Synthetic Errors During Solid-Phase Phosphoramidite Synthesis of Oligonucleotides}},
author = {Yuliya V. Sherstyuk and Ilya S. Dovydenko},
journal = {Molecules},
year = {2026},
month = oct,
doi = {10.3390/molecules31203600},
url = {https://www.mdpi.com/1420-3049/31/20/3600},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Synthetic Errors During Solid-Phase Phosphoramidite Synthesis of Oligonucleotides
AU - Yuliya V. Sherstyuk
AU - Ilya S. Dovydenko
PY - 2026
DA - 2026/10/10
JO - Molecules
DO - 10.3390/molecules31203600
UR - https://www.mdpi.com/1420-3049/31/20/3600
AB - While solid-phase phosphoramidite chemistry remains the gold standard for nucleic acid synthesis, the rigorous purity requirements of modern therapeutic oligonucleotides demand a much tighter control over side reactions. This review critically examines the underlying mechanisms of impurity formation during chain assembly and evaluates practical strategies to mitigate them. We detail key nucleobase degradation pathways, specifically O6-guanine phosphitylation, acrylonitrile-induced alkylation, cytidine deamination, and acid-catalyzed adenine depurination. Furthermore, we address current debates surrounding the capping step, contrasting the sequence errors induced by traditional anhydride-based mixtures with the protective benefits of phosphoramidite-based capping reagents. By mapping these chemical trade-offs and evaluating various protecting group strategies, we emphasize the growing need to shift from universal synthetic cycles toward context-dependent protocols, tailoring reaction conditions to specific sequences to ensure maximum fidelity.
SN - 1420-3049
ER -