DNA Labeling Using DNA Methyltransferases

Chemical Expansion of the Methyltransferase Reaction: Tools for DNA Labeling and Epigenome Analysis

“…This Account describes the development of an enabling technology from a proof-of-principle demonstration to a variety of applications involving targeted covalent derivatization and analysis of DNA 64 (as well as RNA, proteins, and small molecules) 34,65,66 by numerous laboratories worldwide. Ultimately, we propose the first general approach that permits high-resolution genome-wide "tracking" of methylation events carried out by an individual Dnmt enzyme in live mammalian cells.…”

Synthesis of S‐Adenosyl‐L‐Methionine Analogs with Extended Transferable Groups for Methyltransferase‐Directed Labeling of DNA and RNA

“…These cofactors permitted efficient and targeted transfer of extended side chains using MTases as directing vehicles (approach named methyltransferase-directed transfer of activated groups, mTAG (Lukinavičius et al, 2007)). A series of cofactor analogs have been designed and proved suitable for labeling a variety of biological targets in DNA, RNA, and proteins (for recent reviews see Bollu et al, 2022;Tomkuvienė et al, 2019Tomkuvienė et al, , 2022. We mostly focused on designing AdoMet analogs with triple bond-containing side chains carrying a terminal functional group, which proved particularly efficient with DNA cytosine-5 MTases.…”

“…This cofactor, named Ado-6-azide, proved of high utility for targeted mTAG labeling of DNA or RNA in vitro, in bacterial cell lysates and in live mammalian cells (Lukinavičius et al, 2012(Lukinavičius et al, , 2013Plotnikova et al, 2014;Stankevičius et al, 2022). Another presented AdoMet analog bears a deuterium labeled ethyl-2,2,2-d 3 group, which can also be transferred by many MTases akin to the conventional ethyl group (Dalhoff, Lukinavičius et al, 2006;Tomkuvienė et al, 2022). The synthetic strategy involves a direct chemoselective alkylation of S-adenosyl-L-homocysteine (AdoHcy) under mild acidic conditions, which render transient protection of all N-nucleophilic positions in AdoHcy (Fig.…”