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Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors

Hildebrand, Samuel R
Hedger, Adam K
Yamada, Ken
Watts, Jonathan K
Khvorova, Anastasia
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Journal Article
Publication Date
2023-04-14
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04/14/2024
Abstract

Preadenylated single-stranded DNA ligation adaptors are essential reagents in many next generation RNA sequencing library preparation protocols. These oligonucleotides can be adenylated enzymatically or chemically. Enzymatic adenylation reactions have high yield but are not amendable to scale up. In chemical adenylation, adenosine 5'-phosphorimidazolide (ImpA) reacts with 5' phosphorylated DNA. It is easily scalable but gives poor yields, requiring labor-intensive cleanup steps. Here, we describe an improved chemical adenylation method using 95% formamide as the solvent, which results in the adenylation of oligonucleotides with >90% yield. In standard conditions, with water as the solvent, hydrolysis of the starting material to adenosine monophosphate limits the yields. To our surprise, we find that rather than increasing adenylation yields by decreasing the rate of ImpA hydrolysis, formamide does so by increasing the reaction rate between ImpA and 5'-phosphorylated DNA by ∼10-fold. The method described here enables straightforward preparation of chemically adenylated adapters with higher than 90% yield, simplifying reagent preparation for NGS.

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Hildebrand SR, Hedger AK, Yamada K, Watts JK, Khvorova A. Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors. RNA. 2023 Jul;29(7):1077-1083. doi: 10.1261/rna.079521.122. Epub 2023 Apr 14. PMID: 37059467; PMCID: PMC10275264.

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DOI
10.1261/rna.079521.122
PubMed ID
37059467
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Copyright 2023 Hildebrand et al. This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribu- tion-NonCommercial 4.0 International), as described at http://creative- commons.org/licenses/by-nc/4.0/