Retracted Article: Convenient synthesis of pyrimidine 2‚Ä?deoxyribonucleoside monophosphates with important epigenetic marks at the 5-position
Authors: Dawanna S White
Alyson M Curry
Ai Tran
Yana Cen
Song Zheng
Journal: Organic & Biomolecular Chemistry (2020)
Discipline: CHEMISTRY
Keywords: DNA damage; 5-methylcytosine; epigenetic reprogramming; nucleobases; 32P-postlabeling
Affiliations: Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, USA, Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Institute for Structural Biology

Abstract:  Methyl groups of thymine and 5-methylcytosine (5mC) bases in DNA undergo endogenous oxidation damage. Additionally, 5mC residues can be enzymatically deaminated or oxidized through either genetic alterations or the newly identified epigenetic reprogramming pathway. Several methods have been developed to measure the formation of modified DNA nucleobases including 32P-postlabeling. However, the postlabeling method is often limited by the absence of authentic chemical standards. The synthesis of monophosphate standards of nucleotide oxidation products is complicated by the presence of additional functional groups on the modified bases that require complex protection and deprotection strategies. Due to the emerging interest in the pyrimidine oxidation products, the corresponding protected 3'-phosphoramidites needed for solid-phase oligonucleotide synthesis have been reported, and several are commercially available. We report here an efficient synthesis of 3'-monophosphates from 3'-phosphoramidites and the subsequent enzymatic conversion of 3'-monophosphates to the corresponding 5'-monophosphates using commercially available enzymes. 

Retracted: Yes

PubPeer comments:
 Copy pasted from https: doi.org 10.1039 D1OB90019F :  Retraction of u2018Convenient synthesis of pyrimidine 2u2032-deoxyribonucleoside monophosphates with important epigenetic marks at the 5-positionu2019 by Song Zheng et al., Org. Biomol. Chem., 2020, 18, 5164u20135173, DOI: 10.1039 D0OB00884B The Royal Society of Chemistry hereby wholly retracts this Organic Biomolecular Chemistry article due to concerns about the reproducibility of the data. The Royal Society of Chemistry has been contacted by the authors of this article to alert us that recent experiments by their group have shown that some results are not reproducible, especially the yields of several key intermediates. Given the focus on the easy access to epigenetically important nucleoside monophosphates, unreliable yields significantly impact confidence in the results. Ahead of a thorough re-examination of the entire study, in order to preserve the rigor of the scientific record, the signing authors have chosen to retract the article and they would like to apologise for any inconvenience this may have caused for readers. Signed: Song Zheng, Ai Tran, Alyson M. Curry, Dawanna S. White and Yana Cen, 9th February 2021. Retraction endorsed by Katie Lim, Executive Editor, Organic Biomolecular Chemistry. First published 25 Feb 2021. See for backgrounds https: retractionwatch.com 2021 03 10 drug-researchers-retract-two-papers-one-because-human-stem-cells-were-actually-mouse-stem-cells ,