Preparation of a 4′‐Thiouridine Building‐Block for Solid‐Phase Oligonucleotide Synthesis

Benckendorff, Caecilie M. M.; Sanghvi, Yogesh S.; Miller, Gavin J.

Abstract

Starting from a commercially available thioether, we report a nine‐step synthesis of a 4′‐thiouridine phosphoramidite building‐block. We install the uracil nucleobase using Pummerer‐type glycosylation of a sulfoxide intermediate followed by a series of protecting group manipulations to deliver the desired phosphite. Notably, we introduce a 3′,5′‐O‐di‐tert‐butylsilylene protecting group within a 4′‐thiosugar framework, harnessing this to ensure regiospecific installation of the 2′‐O‐silyl protecting group. We envisage this methodology will be generally applicable to other 4′‐thionucleosides and duly support the exploration of their inclusion within related nucleic acid syntheses. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: (2R,3S,4R)‐2,3‐O‐Isopopropylidene‐5‐O‐tert‐butyldiphenylsilyl‐1‐(4‐sulfinyl)cyclopentane: Sulfoxidation Basic Protocol 2: 2′,3′‐O‐Isopropylidene‐5′‐O‐tert‐butyldiphenylsilyl‐4′‐thiouridine: Pummerer glycosylation Basic Protocol 3: 4′‐Thiouridine: Deprotection Basic Protocol 4: 2′‐O‐tert‐Butyldimethylsilyl‐3′,5′‐di‐tert‐butylsiloxy‐4′‐thiouridine: 2′,3′,5′‐O‐silylation Basic Protocol 5: 2′‐O‐tert‐Butyldimethylsilyl‐4′‐thiouridine: Selective 3′‐5′‐desilylation Basic Protocol 6: 2′‐O‐tert‐Butyldimethylsilyl‐5′‐O‐dimethoxytrityl‐4′‐thiouridine: 5′‐O‐dimethoxytritylation Basic Protocol 7: 2′‐O‐tert‐butyldimethylsilyl‐3′‐O‐[(2‐cyanoethoxy)(N, N‐diisopropylamino)phosphino]‐5′‐O‐dimethoxytrityl‐4′‐thiouridine: 3′‐O‐phosphitylation

• Journal Article Type: Article
• Acceptance Date: Sep 1, 2023
• Online Publication Date: Sep 25, 2023
• Publication Date: Sep 1, 2023
• Deposit Date: Oct 9, 2023
• Publicly Available Date: Oct 9, 2023
• Journal: Current Protocols
• Print ISSN: 1934-8576
• Publisher: Wiley
• Peer Reviewed: Peer Reviewed
• Volume: 3
• Issue: 9
• Pages: e878
• DOI: https://doi.org/10.1002/cpz1.878
• Keywords: thiosugar, protecting group, phosphoramidite, 4′‐thionucleoside