Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking

Ivancová, Ivana; Leone, Denise‐Liu'; Hocek, Michal

doi:10.1016/j.cbpa.2019.07.007

Cited by 42 publications

(25 citation statements)

References 79 publications

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“…As a result, target TPyzPzs ( 1 – 8 , Figure ) are of low‐symmetrical character with only one quarter decorated with functional groups. Regarding the functional groups, carboxy group, azide moiety and hydroxy group were chosen for this series based on the typical procedures for binding molecules to ODN probes . For example, azide moiety in TPyzPzs 3 and 7 may be used to attach the quencher to a solid phase (CPG) which may be followed by ODN synthesis resulting in an ODN probe with a quencher at its 3′ end.…”

Section: Resultsmentioning

confidence: 99%

“…The binding of synthetic molecules to various biomolecules and their subsequent use in different fields, such as biochemistry, molecular biology, medicinal chemistry, and environmental analysis, represent a current trend in basic research and in practice . Detailed understanding of the structure of DNA and the elucidation of its functions have led to the development of many helpful biochemical assays.…”

Section: Introductionmentioning

confidence: 99%

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Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

et al. 2020

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Though tetrapyrazinoporphyrazines (TPyzPzs) are generally presented as universal dark quenchers for oligonucleotide probes, the availability of TPyzPzs bearing different functional groups suitable for attachment to 3′, and 5′ ends or intrastrand positions remains rather limited. Therefore, a synthetic route to hexa(bis(2‐methoxyethyl)amino) or hexa(diethylamino) TPyzPzs functionalized by an azide, hydroxy, or carboxy group or their combinations was developed. Studies of self‐assembly into J‐dimers in nonpolar solvents and their stability upon titration with pyridine (association constants, KP values, ranging 0.32–12.7×102 M−1) revealed that smaller peripheral substituents and functionalization of TPyzPzs improves the stability of J‐dimers. ΦΔ and ΦF were low for the monomers (ΦF<0.0001, ΦΔ<0.008, DMF) due to quenching by intramolecular charge transfer; however, they increased in nonpolar solvents and after self‐assembly into J‐dimer (up to ΦF=0.027, ΦΔ=0.28).

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

et al. 2020

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“…Furthermore, we would like to point out recent reviews about post-synthetic labeling of DNA and RNA. 29,33,[59][60][61][62][63] 2.1 Direct chemical labeling via solid-phase synthesis Solid-phase synthesis is the method of choice to make labeled RNA and DNA of up to 150-200 nucleotides. 64 This approach uses nucleoside phosphoramidites as key building blocks and is compatible with almost any natural or non-natural modification as long as undesired side reactions during synthesis are avoided and reactive hydroxyl and amino groups can be protected.…”

Section: Fluorescent Labeling Of Nucleic Acidsmentioning

confidence: 99%

“…However, we would like to mention that numerous typical conjugation chemistries, using thiols, amines 84 and maleimides 85 have also been successfully combined with solid-phase synthesis. For a more detailed overview, we recommend the reviews from Madsen et al and Ivancová et al 29,86 Various functional handles like terminal alkynes, 87,88 cyclooctynes 89,90 and norbornenes 91 were successfully incorporated during solid-phase synthesis without the necessity of additional protection chemistry. Fluorescent labeling was then achieved in a second step by click chemistry.…”

Section: Two-step Chemical Labeling Via Solid-phase Synthesismentioning

confidence: 99%

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Covalent labeling of nucleic acids

2020

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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.I nvolving chemical partners that specifically react together in highly complex biological fluids,t his branch of chemistry nowa llows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies.C hemical reporter strategies include metabolic glycan labelling,s ite-specific incorporation of unnatural amino acids in proteins,and post-synthetic labelling of nucleic acids.W hile amajority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes amore 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,w ediscuss 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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Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking

Cited by 42 publications

References 79 publications

Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

Synthesis and J‐Dimer Formation of Tetrapyrazinoporphyrazines with Different Functional Groups for Potential Biomolecular Probe Applications

Covalent labeling of nucleic acids

To View Your Biomolecule, Click inside the Cell

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