59090-48-1

Usage

Uses

Used in Chemical Biology and Bioorthogonal Chemistry:
5-azidomethyl-2'-deoxyuridine is used as a nucleoside analog for probing the dynamics and interactions of DNA. Its incorporation into DNA during synthesis enables researchers to investigate the mechanisms of DNA repair and replication, contributing to a deeper understanding of DNA biology.
Used in Biomedical Research:
5-azidomethyl-2'-deoxyuridine is utilized in the development of new diagnostic tools for the imaging and detection of DNA in biological systems. Its unique azide group allows for selective chemical reactions, facilitating the creation of innovative imaging agents and detection methods that enhance the study of DNA in various biological contexts.
Used in DNA Repair and Replication Studies:
5-azidomethyl-2'-deoxyuridine is employed as a research tool to explore the mechanisms of DNA repair and replication. By incorporating this modified nucleoside into DNA, scientists can gain insights into the processes that maintain genetic integrity and identify potential targets for therapeutic intervention in diseases associated with DNA damage and replication errors.
Used in Development of New Imaging Agents:
5-azidomethyl-2'-deoxyuridine is used as a building block for the synthesis of new imaging agents that can selectively label and visualize DNA in biological systems. The azide group in 5-azidomethyl-2'-deoxyuridine enables bioorthogonal reactions with specific probes, allowing for the development of highly sensitive and selective imaging techniques for studying DNA in vivo.
Used in Drug Development:
5-azidomethyl-2'-deoxyuridine has potential applications in drug development, particularly in the design of targeted therapies for diseases involving DNA abnormalities. Its ability to be incorporated into DNA and its reactivity in bioorthogonal chemistry can be harnessed to develop drugs that specifically interact with or modify DNA, offering new avenues for treating genetic disorders and cancers.

InChI:InChI=1/C10H13N5O5/c11-14-12-2-5-3-15(10(19)13-9(5)18)8-1-6(17)7(4-16)20-8/h3,6-8,11,16-17H,1-2,4H2/p+1

Upstream product

• 5116-24-5 2'-deoxy-5-(hydroxymethyl)uridine 
• 72274-20-5 3′,5′-di-O-acetyl-5-azidomethyl-2′-deoxyuridine 
• 58589-18-7 3',5'-di-O-acetyl-5-bromomethyl-2'-deoxyuridine 
• 35898-30-7 3',5'-di-O-benzoylthymidine 
• 291525-17-2 3′,5′-bis-O-(tert-butyldimethylsilyl)-5-bromomethyl-2'-deoxyuridine 
• 823790-97-2 3',5'-bis-O-(tert-butyldimethylsilyl)-5-(azidomethyl)-2'-deoxyuridine 
• 40733-26-4 3',5'-O-di(tert-butyldimethylsilyl)thymidine 
• 50-89-5 thymidine 
• 6979-97-1 3',5'-diacetylthymidine 
• 825649-02-3 5-(N-methoxymethylamine)-2'-deoxyuridine 

Downstream Products

• 1620130-62-2 5'-O-(4,4'-dimethoxytriphenylmethyl)-5-(4-methylchromen-2-one-1,2,3-triazol-1-yl)methyl-2'-deoxyuridine 
• 263758-82-3 {5:2'-O-[methyleneimino(2-oxoethane-2,1-diyl)]}-linked 5'-O-(4,4'-dimethoxytrityl)-P-thiouridyl-(3'->5')-2'-deoxyuridine 3'-(2-cyanoethyl diisopropylphosphoramidite) S-phenyl ester 
• 263758-81-2 {5:2'-O-[methyleneimino(2-oxoethane-2,1-diyl)]}-linked 5'-O-(4,4'-dimethoxytrityl)-P-thiouridyl-(3'->5')-2'-deoxy-3'-O-(tetrahdyro-2H-pyran-2-yl)uridine S-phenyl ester 
• 263712-30-7 {5:2'-O-[methyleneimino(2-oxoethane-2,1-diyl)]}-linked 5'-O-(4,4'-dimethoxytrityl)-P-thiouridyl-(3'->5')-2'-deoxyuridine S-phenyl ester 
• 886578-12-7 6-[3-O-(tert-butyl(dimethyl)silyl)-2-deoxy-5-O-(4,4'-dimethoxytrityl)-β-D-ribofuranosyl]-3,4-dihydropyrimido[4,5-d]pyrimidine-2,7(1H,6H)-dione 
• 823791-02-2 3'-O-(tert-butyl(dimethyl)silyl)-5'-O-(4,4'-dimethoxytrityl)-5-(azidomethyl)deoxycytidine 
• 823791-01-1 3'-O-(tert-butyl(dimethyl)silyl)-5'-O-(4,4'-dimethoxytrityl)-5-(azidomethyl)deoxyuridine 
• 886578-13-8 6-[2-deoxy-5-O-(4,4'-dimethoxytrityl)-β-D-ribofuranosyl]-3,4-dihydropyrimido[4,5-d]pyrimidine-2,7(1H,6H)-dione 
• 137552-29-5 5-(azidomethyl)-5′-O-(4,4′-dimethoxytrityl)-2′-deoxyuridine 
• 70465-55-3 5-(aminomethyl)-2'-deoxyuridine 

Relevant academic research and scientific papers

Synthesis of a new analog of thymidine for in vivo non-radioactive labeling of DNA

The introduction of 6-(p-bromobenzoylamino)caproyl radical in the methyl group of 2'-O-deoxythymidine is described. In vivo incorporation of this nucleoside to DNA was determined using a monoclonal antibody that recognized the radical.

Multinuclear NMR and kinetic analysis of DNA interstrand cross-link formation

Recently, a phenylselenyl-modified thymidine (2) was shown to produce DNA interstrand crosslinks (ICLs) via two mechanisms. Photolysis of 2 generates 5-(2′-deoxyuridinyl)methyl radical (1), the reactive intermediate that results from formal hydrogen atom abstraction from the thymine methyl group. This reactive intermediate reacts with the opposing dA and is the first example of a DNA radical that produces ICLs. Kinetic competition studies support the proposal that the rate-limiting step in ICL formation from 1 involves rotation about the glycosidic bond and that the rate constant for this process is influenced by the flanking sequence. Cross-links also form with the opposing dA when 2 is treated with mild oxidants that result in the formation of an intermediate methide-like species (4). Kinetic experiments reveal that 4 reacts with azide, a model nucleophile, via an S42′ pathway. Previous experiments suggested that the same product is produced via 1 or 4 but that the initially formed cross-link rearranges during the enzyme digestion and isolation procedures. In situ product analysis by NMR using synthetic, doubly labeled duplex DNA containing 13C-2 and 15N1-dA provides definitive evidence that the kinetic ICL products formed via the radical and oxidative pathways are the same and correspond to that arising from formal alkylation of N1-dA. Furthermore, analysis of the thermodynamic product formed upon rearrangement indicates that the primary product isomerizes via an associative mechanism in DNA.

Electron-Mediated Aminyl and Iminyl Radicals from C5 Azido-Modified Pyrimidine Nucleosides Augment Radiation Damage to Cancer Cells

Two classes of azido-modified pyrimidine nucleosides were synthesized as potential radiosensitizers; one class is 5-azidomethyl-2′-deoxyuridine (AmdU) and cytidine (AmdC), while the second class is 5-(1-azidovinyl)-2′-deoxyuridine (AvdU) and cytidine (AvdC). The addition of radiation-produced electrons to C5-azido nucleosides leads to the formation of π-aminyl radicals followed by facile conversion to σ-iminyl radicals either via a bimolecular reaction involving intermediate α-azidoalkyl radicals in AmdU/AmdC or by tautomerization in AvdU/AvdC. AmdU demonstrates effective radiosensitization in EMT6 tumor cells.

Carborane- or Metallacarborane-Linked Nucleotides for Redox Labeling. Orthogonal Multipotential Coding of all Four DNA Bases for Electrochemical Analysis and Sequencing

We report a series of 2′-deoxyribonucleoside triphosphates bearing dicarba-nido-undecaborate ([C2B9H11]1-), [3,3′-iron-bis(1,2-dicarbollide)]- (FESAN, [Fe(C2B9H11)2]2-) or [3,3′-cobalt-bis(1,2-dicarbollide)]- (COSAN, [Co(C2B9H11)2]2-) groups prepared either through the Sonogashira cross-coupling or the CuAAC click reaction. The modified dNXTPs were substrates for KOD XL DNA polymerase in enzymatic synthesis of modified DNA through primer extension (PEX). The nido-carborane- and FESAN-modified nucleotides gave analytically useful oxidation signals in square-wave voltammetry and were used for redox labeling of DNA. The redox-modified DNA probes were prepared by PEX using tailed primers and were hybridized to electrode (gold or glassy carbon) containing capture oligonucleotides. The combination of nido-carborane- and FESAN-linked nucleotides with 7-ferrocenylethynyl-7-deaza-dATP and 7-deaza-dGTP allowed polymerase synthesis of DNA fully modified at all four nucleobases, and each of the redox labels gave four differentiable and ratiometric signals in voltammetry. Thus, the combination of these four redox labels constitutes the first fully orthogonal redox coding of all four canonical nucleobases, which can be used for determination of nucleobase composition of short DNA stretches in one simple PEX experiment with electrochemical readout.

One-step to get 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine and detection of it through click reaction

Nowadays a few ways to synthesize 5-azidomethyl-2′-deoxyuridine from 5-hydroxymethyl-2′-deoxyuridine have been reported. But none of them was one-step. And many of them need to protect the hydroxyl group on the pentose ring. The detection of 5-hydroxymethyl-2′-deoxyuridine is also very important in many biological processes. However few fluorescence detection strategies have been tried to do this. Herein, we reported a one-step protocol to synthesize 5-azidomethyl-2′-deoxyuridine, which was then used for detecting 5-hydroxymethyl-2′-deoxyuridine through a click reaction.

Oxygen independent DNA interstrand cross-link formation by a nucleotide radical

A 5-(2′-Deoxyuridinyl)methyl radical (1) was independently generated from three photochemical precursors and is the first example of a DNA radical that forms interstrand cross-links. Oxygen labeling experiments support generation of 1 by all precursors. I

Synthesis and properties of oligothymidylates incorporating an artificial bend motif

The uridylyl-(3' → 5')-thymidine dinucleotide block 14 (cUpdU), having a cyclic structure between the 2'-hydroxy of the upstream uridine and the 5- substituent of the downstream thymidine, was synthesized (Schemes 1 and 2). This cyclic structure is a stab

Synthesis and Biological Activities of 5-(Hydroxymethyl, azidomethyl, or aminomethyl)-2'-deoxyuridine and Related 5'-Substituted Analogues

The synthesis of 5-(azidomethyl)-2'-deoxyuridine (10) has been accomplished by two independent methods.The first involved tosylation of 5-(hydroxymethyl)-2'-deoxyuridine (1) to furnish a mixture of two mono- and a ditosyl nucleosides which were converted into the corresponding 5-(azidomethyl) (10), 5-(azidomethyl)-5'-azido (14), and 5-(hydroxymethyl)-5'-azido (15) derivatives of 2'-deoxyuridine.The second method was more selective and required the formation of the intermediate 5-(bromomethyl)-3',5'-di-O-acetyl-2'-deoxyuridine (8), followed by displacement of the bromo group by lithium azide and deacetylation.Catalytic hydrogenation of the azides 9, 10, 14, and 15 gave the corresponding amines 16, 2, 6, and 7, repectively.Compounds 1, 2, 10, and 16 inhibited the growth of murine Sarcoma 180 and L1210 in culture, and the activity of 2 was prevented by 2'-deoxypyrimidine nucleosides by not by purine nucleosides.The replication of herpes simplex virus type 1 (HSV-1) was strongly inhibited only by 1 and 10.Studies on the binding of the various thymidine analogues to HSV-1 encoded pyrimidine deoxyribonucleoside kinase indicate that 1 and 10 have good affinity for the enzyme.