Covalent labeling of nucleic acids

Klöcker, Nils; Weissenboeck, Florian P; Rentmeister, Andrea

doi:10.1039/d0cs00600a

Cited by 100 publications

(122 citation statements)

References 239 publications

(273 reference statements)

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“…Intracellular by essence,t he use of chemical reporter strategies to label and track DNAo rR NA in the cellular environment has been extensively reviewed, and we refer the reader to two recent reviews by the groups of Wagenknecht and Rentmeister for more comprehensive details. [123,124] Focusing here on metabolic labelling approaches,desoxyuridine and uridine reporters containing apropargyl group for in vivo visualization of both DNAa nd RNAwere originally described by Salic and co-workers. [125,126] Thedeoxythymidine analogue EdU,b earing an ethynyl group at position 5 (Scheme 7), has since become the reporter of choice for DNAm etabolic marking and can, for example,b eu sed in combination with profluorescent azide probes.…”

Section: Targeting Nucleic Acids With Bioorthogonal Chemistrymentioning

confidence: 99%

To View Your Biomolecule, Click inside the Cell

2021

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The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site‐specific incorporation of unnatural amino acids in proteins, and post‐synthetic labelling of nucleic acids. While a majority of literature reports mark cell‐surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off‐target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.

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Section: Targeting Nucleic Acids With Bioorthogonal Chemistrymentioning

confidence: 99%

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2021

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“…The approach and nucleotide building blocks can be now applied in construction of reactive DNA probes for cross-linking to Arg-containing DNA-binding proteins, for synthesis of stable DNA-peptide or DNA-protein conjugates, [4,5] as well as for post-synthetic labelling of DNA. [6]…”

Section: Angewandte Chemiementioning

confidence: 99%

“…In addition, covalent protein-DNA conjugates are also useful for other applications in chemical biology, biosensing [4] or targeting of therapeutic nucleic acids [5] and therefore new efficient bioconjugation methods are highly desirable. [6] There are some widely-used non-specific cross-linking methods, typically based on photochemical generation of reactive species, that is, radicals [7] or carbenes [8] in DNA that crosslink randomly to any amino acids. More useful but also challenging are amino acid-specific cross-linking reactions and there were only handful of them reported for DNAprotein cross-linking.…”

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confidence: 99%

1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins

et al. 2021

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Linear or branched 1,3-diketone-linked thymidine 5'-O-mono-and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5dioxohexyl group (HDO) efficiently reacted with argininecontaining peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).

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“…Post‐synthetic modifications utilize easy‐to‐obtain ONs bearing reactive handles to introduce desired labels under mild conditions (Madsen & Gothelf, 2019). Although various reactions have been used to synthesize ONs modified through post‐synthetic strategies, the methods to generate ONs with nucleobase‐conjugated pi‐system modifications are still limited (Klocker et al., 2020; Zhang et al., 2019).…”

Section: Commentarymentioning

confidence: 99%

Post‐Synthetic Modification of Oligonucleotides Through Oxidative Amination of 4‐Thio‐2′‐Deoxyuridine

et al. 2021

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Functionalized oligonucleotides (ONs) are widely applied as target recognition molecules for biosensing and gene regulation. Herein, we describe a general method for post-synthetic modification of ONs based on the oxidative amination of 4-thio-2 -deoxyuridine (4SdU) with sodium periodate and several amines. Alkyne-/azide-, biotin-, and fluorophore-modified ONs were prepared by modifying 4SdU-containing ONs with the corresponding amines and characterized for their bioorthogonal reactivity, streptavidin-binding affinity, and fluorescence properties, respectively. We synthesized three fluorophoremodified ONs with and without the aromatic fluorophores conjugated to modified nucleobases and investigated their emission properties.

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Covalent labeling of nucleic acids

Abstract: Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells.

Cited by 100 publications

References 239 publications

To View Your Biomolecule, Click inside the Cell

To View Your Biomolecule, Click inside the Cell

1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins

Post‐Synthetic Modification of Oligonucleotides Through Oxidative Amination of 4‐Thio‐2′‐Deoxyuridine

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