Chemoselective Modification of Vinyl DNA by Triazolinediones

Palladium-Catalyzed C-H Olefination for Nucleic Acid Production

The palladium-catalyzed direct C-H olefination of unprotected uridine, 2'-deoxyuridine, uridine monophosphate, and uridine analogues are described here. This protocol provides an efficient, atom-economical, and environmentally friendly method for the introduction of an alkenyl group at the C5 position of the uracil without pre-functionalization. A series of C5-alkenylated uridine analogues, including some biologically significant compounds and potential pharmaceutical candidates, were synthesized with exposed hydroxyl groups on the ribose. © 2023 Wiley Periodicals LLC. Basic Protocol 1: The reaction of uridine, 2'-deoxyuridine, and sofosbuvir for the C-H olefination with methyl acrylate Basic Protocol 2: The reaction of uridine and 2'-deoxyuridine for the C-H olefination with styrene.

Formal [4 + 2] Cycloadditions of Maleimides on Duplex DNA

Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2'-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU-maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2'-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels-Alder cycloaddition. VdU-maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.

Palladium-catalyzed C-H olefination of uridine, deoxyuridine, uridine monophosphate and uridine analogues

The palladium-catalyzed oxidative C-H olefinations of uridine, deoxyuridine, uridine monophosphate and uridine analogues are reported herein. This protocol provides an efficient, atom-economic and environmentally friendly approach to the synthesis of biologically important C5-alkene modified uracil/uridine-containing derivatives and pharmaceutical candidates.

A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids

Chemical modification of nucleic acids in living cells can be sterically hindered by tight packing of bioorthogonal functional groups in chromatin. To address this limitation, we report here a dual enhancement strategy for nucleic acid-templated reactions utilizing a fluorogenic intercalating agent capable of undergoing inverse electron-demand Diels-Alder (IEDDA) reactions with DNA containing 5-vinyl-2'-deoxyuridine (VdU) or RNA containing 5-vinyl-uridine (VU). Reversible high-affinity intercalation of a novel acridine-tetrazine conjugate "PINK" (K_D =5±1 μM) increases the reaction rate of tetrazine-alkene IEDDA on duplex DNA by 60 000-fold (590 M^-1  s^-1 ) as compared to the non-templated reaction. At the same time, loss of tetrazine-acridine fluorescence quenching renders the reaction highly fluorogenic and detectable under no-wash conditions. This strategy enables live-cell dynamic imaging of acridine-modified nucleic acids in dividing cells.

1,2-Disubstituted 1,2-Dihydro-1,2,4,5-tetrazine-3,6-dione as a Dynamic Covalent Bonding Unit at Room Temperature

Dynamic covalent bonds are useful tools in a wide range of applications. Although various reversible chemical reactions have been studied for this purpose, the requirement for harsh conditions, such as high temperature and low or high pH, to activate generally stable covalent bonds limits their potential applications involving biomolecules or household utilization. Here, we report the design, synthesis, characterization, and dynamic covalent bonding properties of 1,2-disubstituted 1,2-dihydro-1,2,4,5-tetrazine-3,6-dione (TETRAD). Hetero-Diels-Alder reactions of TETRAD with furan derivatives and their retro-reactions proceeded rapidly at room temperature under neutral conditions, enabling a chemically induced sol-gel transition system.

[4+2] and [2+4] cycloaddition reactions on single- and double-stranded DNA: a dual-reactive nucleoside

Here we report dual reactivity of diene-modified duplex DNA containing 5-(1,3-butadienyl)-2'-deoxyuridine “BDdU”. Regular-electron demand [4+2] cycloaddition proceeded upon addition of a maleimide, whereas inversed-electron demand [2+4] cycloaddition occurred upon addition...

Exploiting Urazole's Acidity for Fabrication of Hydrogels and Ion-Exchange Materials

In this study, the acidity of urazole (pKa 5-6) was exploited to fabricate a hydrogel in two simple and scalable steps. Commercially available poly(hexamethylene)diisocyanate was used as a precursor to synthesize an urazole containing gel. The formation of urazole was confirmed by FT-IR and 1H-NMR spectroscopy. The hydrogel was characterized by microscopy imaging as well as spectroscopic and thermo-gravimetric analyses. Mechanical analysis and cell viability tests were performed for its initial biocompatibility evaluation. The prepared hydrogel is a highly porous hydrogel with a Young's modulus of 0.91 MPa, has a swelling ratio of 87%, and is capable of exchanging ions in a medium. Finally, a general strategy was demonstrated to embed urazole groups directly into a crosslinked material.

Water-Involved Ring-Opening of 4-Phenyl-1,2,4-triazoline-3,5-dione for "Photo-Clicked" Access to Carbamoyl Formazan Photoswitches In Situ

Cyclic azodicarbonyl derivatives, particularly 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD), commonly serve as arenophile, dienophile, enophile and electrophile. Perplexed by its instability in aqueous environment, there are few studies focused on the transient intermediate produced by hydrolysis of PTAD to achieve synthetic significance. Herein, we describe a "photo-click" method that involves nitrile imine (NI) from diarylsydnone to capture the diazenecarbonyl-phenyl-carbamic acid (DACPA) generated by water-promoted ring-opening of PTAD. DFT calculation reveal that H-bonding interactions between PTAD and water are vital to form DACPA which exhibited an umpolung effect during ligation by nature bond orbit (NBO) analysis. The ultra-fast ligation resulted in carbamoyl formazans, as a unique Z↔E photo-switchable linker on target molecules, including peptide and drugs, with excellent anti-fatigue performance. This strategy is showcased to construct highly functionalized carbamoyl formazans in situ for photo-pharmacology and material studies, which also expands the chemistry of PTAD in aqueous media.

Direct and selective metal-free N6-arylation of adenosine residues for simple fluorescence labeling of DNA and RNA

We have developed an unprecedented transition metal-free approach for the direct fluorescence turn-on labeling of natural oligonucleotides through selective N6-arylation of adenosine moieties. This method allows the simple and direct fluorescence labeling of natural unmodified DNA and RNA, but is dependent on the secondary structure, favoring single-stranded structures.

Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides

Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.

Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state

To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.

Cross-linking cellular nucleic acids via a target-directing double click reagent

Bioorthogonal ligation reactions are powerful tools for characterizing DNA metabolism, DNA-protein binding interactions, and they even provide new leads for therapeutic strategies. Nucleoside analogs can deliver bioorthogonal functional groups into chromatin via cellular metabolic pathways, however, insufficient phosphorylation by endogenous kinases often limits the efficiency of their incorporation. Even when successfully metabolized into biopolymers, steric hindrance of the modified nucleotide by chromatin can inhibit subsequent click reactions. In this chapter, we describe methods that overcome these limitations. Nucleotide monophosphate triesterers can bypass the need for cellular nucleoside kinase activity and thereby enable efficient incorporation of azide groups into cellular DNA. Steric access to and modification of the azide groups within natively folded chromatin can then be accomplished using a bioorthogonal "intercalating reagent" comprised of a cationic Sondheimer diyne that reversibly intercalates into duplexes where it undergoes tandem, strain-promoted cross-linking of two azides to give DNA-DNA interstrand crosslinks or DNA-fluorophore conjugation, depending on the relative number and spatial orientation of the azide groups in the DNA.

A Versatile Catalyst-Free Perfluoroaryl Azide-Aldehyde-Amine Conjugation Reaction

A tri-component reaction, involving an electrophilically-activated perfluoroaryl azide, an enolizable aldehyde and an amine, reacts readily at room temperature without any catalysts in solvents including aqueous conditions to yield a stable amidine conjugate. The versatility of this reaction is demonstrated in the conjugation of an amino acid without prior protection of the carboxyl group, and in the synthesize antibiotic-nanoparticle conjugates.

Bio-orthogonal chemistry-based method for fluorescent labelling of ribosomal RNA in live mammalian cells

A bio-orthogonal chemistry-based approach for fluorescent labelling of ribosomal RNA is described.

Mechanistical Insights into the Bioconjugation Reaction of Triazolinediones with Tyrosine

The bioconjugation at tyrosine residues using cyclic diazodicarboxamides, especially 4-substituted 3 H-1,2,4-triazole-3,5(4 H)-dione (PTAD), is a highly enabling synthetic reaction because it can be employed for orthogonal and site-selective (multi)functionalizations of native peptides and proteins. Despite its importance, the underlying mechanisms have not been thoroughly investigated. The reaction can proceed along four distinctive pathways: (i) the S_EAr path, (ii) along a pericyclic group transfer pathway (a classical ene reaction), (iii) along a stepwise reaction path, or (iv) along an unusual higher order concerted pericyclic mechanism. The product mixtures obtained from reactions of PTAD with 2,4-unsubstituted phenolate support the S_EAr mechanism, but it remains unclear if other mechanisms also take place. In the present work, the various mechanisms are compared using high-level quantum chemistry approaches for the model reaction of 4 H,3 H-1,2,4-triazole-3,5(4 H)-dione (HTAD) with p-cresol and p-cresolate. In a protic solvent (water), the barriers of the S_EAr mechanism and the ene reaction are similar but still too high to explain the available experimental observations. This is only possible if the S_EAr reaction of cresolate with HTAD is taken into account for which nearly vanishing barriers are computed. This satisfactorily explains measured conversion rates in buffered aqueous solutions and the strong activation effects observed upon addition of bases.

Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA

Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(β-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary β-sulfonylvinylamines gave 5-(β-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5'-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions.