5626-99-3

Basic information

• Product Name: 5,6-DIHYDRODEOXYURIDINE
• Synonyms: 5,6-DIHYDRO-2'-DEOXYURIDINE;5,6-DIHYDRODEOXYURIDINE;Dihydrodeoxyuridine;2'-Deoxy-5,6-dihydrouridine
• CAS NO: 5626-99-3
• Molecular Formula: C₉H₁₄N₂O₅
• Molecular Weight: 260.2
• Mol File: 5626-99-3.mol

Chemical Properties

• Boiling Point: 481.1°Cat760mmHg
• Flash Point: 244.7°C
• Appearance: /
• Density: 1.31g/cm³
• Vapor Pressure: 2.06E-09mmHg at 25°C
• Refractive Index: 1.638
• Storage Temp.: −20°C
• Solubility: Methanol (Slightly), Water (Slightly)
• CAS DataBase Reference: 5,6-DIHYDRODEOXYURIDINE(CAS DataBase Reference)
• NIST Chemistry Reference: 5,6-DIHYDRODEOXYURIDINE(5626-99-3)
• EPA Substance Registry System: 5,6-DIHYDRODEOXYURIDINE(5626-99-3)

Safety Data

• WGK Germany: 3
• Hazardous Substances Data: 5626-99-3(Hazardous Substances Data)

Usage

Uses

Used in Molecular Biology Applications:
5,6-Dihydro-2''-deoxyuridine is used as a screening agent for binding to a nucleic acid target, such as an RNA or relevant fragment thereof, which may be implicated in a disease, disorder, or condition. This interaction can help identify potential therapeutic targets and contribute to the development of new treatments.
Used in Pharmaceutical Applications:
In the pharmaceutical industry, 5,6-Dihydro-2''-deoxyuridine is used as a key component in the development of drugs targeting RNA-related diseases. Its ability to bind to specific RNA sequences allows for the creation of targeted therapies that can potentially treat a wide range of conditions, including viral infections and genetic disorders.
Used in Diagnostic Applications:
5,6-Dihydro-2''-deoxyuridine can also be employed in the development of diagnostic tools, such as tests that detect the presence of specific RNA sequences in a patient's sample. This can aid in the early detection and diagnosis of diseases, enabling more timely and effective treatment.

InChI:InChI=1/C18H13N3O4/c22-18-16(12-19-14-6-2-1-3-7-14)20-17(25-18)10-9-13-5-4-8-15(11-13)21(23)24/h1-12,19H

Upstream product

• 951-78-0 2'-deoxyuridine 

Downstream Products

• 504-07-4 5,6-dhydrouracil 
• 1219141-72-6 C₃₀H₃₂N₂O₇ 
• 31962-88-6 2'-deoxytetrahydrouridine 

Relevant articles and documents

A Combined Experimental and Theoretical Approach to the Photogeneration of 5,6-Dihydropyrimidin-5-yl Radicals in Nonaqueous Media

The chemical fate of radical intermediates is relevant to understand the biological effects of radiation and to explain formation of DNA lesions. A direct approach to selectively generate the putative reactive intermediates is based on the irradiation of photolabile precursors. But, to date, radical formation and reactivity have only been studied in aqueous media, which do not completely mimic the microenvironment provided by the DNA structure and its complexes with proteins. Thus, it is also important to evaluate the photogeneration of nucleoside-based radicals in nonaqueous media. The attention here is focused on the independent generation of 5,6-dihydropyrimidin-5-yl radicals in organic solvent through the synthesis of new lipophilic tert-butyl ketone precursors. Formation of 5,6-dihydro-2′-deoxyuridin-5-yl and 5,6-dihydrothymidin-5-yl radicals has first been confirmed by using a new nitroxide-derived profluorescent radical trap. Further evidence has been obtained by nanosecond laser flash photolysis through detection of long-lived transients. Finally, the experimental data are corroborated by multiconfigurational ab initio CASPT2//CASSCF methodology.

USES OF DIHYDRO BASES

The present invention provides pharmaceutical compositions comprising a dihydro base described herein (e.g., compound DHdC). The dihydro base may show multiple tautomerism and may increase mutation of an RNA and/or DNA of a virus or cancer cell. The dihydro base may be used to reduce DNA methylation (e.g., in a cancer cell). The present invention also provides kits including the inventive pharmaceutical compositions and methods of treating a viral infection (e.g., influenza, HIV infection, or hepatitis C) or cancer using the pharmaceutical compositions or kits.

Direct strand scission from a nucleobase radical in RNA

"Chemical equation presented" RNA oxidation is important in the etiology of disease and as a tool for studying the structure and folding kinetics of this biopolymer. Nucleobase radicals are the major family of reactive intermediates produced in RNA exposed to diffusible species such as hydroxyl radical. The nucleobase radicals are believed to produce direct strand breaks by abstracting hydrogen atoms from their own and neighboring ribose rings. By independently generating the formal C5 hydrogen atom addition product of uridine in RNA, we provide the first chemical characterization of the pathway for direct strand scission from an RNA nucleobase radical. The process is more efficient under anaerobic conditions. The preference for strand scission in double-stranded RNA over single-stranded RNA suggests that this chemistry may be useful for analyzing the secondary structure of RNA in hydroxyl radical cleavage experiments if they are carried out under anaerobic conditions.

Synthesis of deoxytetrahydrouridine

The α-hydroxyamido functionality of 2 -deoxytetrahydrouridine (dTHU) makes this seemingly simple and generally useful compound difficult to obtain. Reported synthetic strategies produce extremely poor yields and multiple products, and full characterization data is not available. Described herein is a two-step approach for synthesizing dTHU in increased yields and purity; stability concerns are also addressed. Catalytic reduction (5% Rh/alumina) of 2 deoxyuridine, followed by reduction with sodium borohydride as a limiting reagent, produces dTHU and limits formation of side products. Evidence was obtained for formation of a methoxy-substituted analogue during purification. By this strategy, dTHU of >95% purity can be obtained in 40% yield on a 150 mg scale.

Selective fluorescence-based detection of dihydrouridine with boronic acids

The first fluorescent sensing system for dihydrouridine detection is presented. Dihydrouridine is the single most frequently occurring post-transcriptional modification in tRNA from bacteria and eukaryotes. A series of 10 boronic acid derivatives was prepared and their fluorogenic behaviours towards dihydrouridine and uridine were investigated. Whereas uridine always quenches fluorescence via π-π stacking interactions, several boronic acid sensors have been found to show substantial fluorescence enhancement upon binding with dihydrouridine.

β-Selective synthesis of 2′-deoxy-5,6-dihydro-4-thiouridine, a precursor of the unstable nucleoside product of ionising radiation damage 2′-deoxy-5,6-dihydrocytidine

4-Thio oxathiaphosphepane nucleosides 2-4 undergo a rearrangement in pyridine that leads selectively to the β anomer of the 2′-deoxy-5,6- dihydro-4-thiouridine derivative 5. This diastereoselective reaction proceeds through a multistep mechanism initiated

Independent generation and study of 5,6-dihydro-2′-deoxyuridin-6-yl, a member of the major family of reactive intermediates formed in DNA from the effects of γ-radiolysis

Nucleobase radicals are the major family of reactive intermediates formed when nucleic acids are exposed to γ-radiolysis. Elucidation of their reactivity is complicated by the formation of multiple species randomly throughout the biopolymers. 5,6-Dihydro-2′-deoxyuridin-6-yl (1) was generated upon photolysis (350 nm) of the respective tert-butyl ketone (2). The radical abstracts hydrogen atoms from β-mercaptoethanol (k = 8.8 ± 0.5 × 106 M-1 s-1) and 2,5-dimethyltetrahydrofuran (k = 31 ± 2.5 M-1 s-1). The latter was used as a model for the 2-deoxyribose component of DNA. The major product formed in the presence of O2 was 6-hydroxy-5,6-dihydro-2′-deoxyuridine (11), which is believed to be formed directly from the peroxy precursor and not via elimination of superoxide. Small amounts of 2-deoxyribonolactone (13) were also formed under aerobic conditions. This product is believed to result from intramolecular hydrogen atom abstraction by the C6-peroxyl radical (14) and suggests that γ-radiolysis may indirectly result in oxidation of the C1′-position of nucleotides, despite the inaccessibility of this hydrogen in duplex DNA.

DNA damage induced via 5,6-dihydrothymid-5-yl in single-stranded oligonucleotides

5,6-Dihydrothymid-5-yl (4) is generated via Norrish type I cleavage of isopropyl ketone 7. Ketone 7 was site specifically incorporated into chemically synthesized polythymidylates and an oligonucleotide containing all four native deoxyribonucleotides. No