2-Deoxyuridine , CAS No.21052-20-0

CAS: 21052-20-0 Cat. No.: D1425542 Summenformel: C₉H₁₂N₂O₅ Molekulargewicht: 228.20

Storage

Store at -20°C

Shipped In

Ice chest + Ice pads

Übersicht

2-Deoxyuridine is a purine nucleoside analog. Purine nucleoside analogs have broad antitumor activity targeting indolent lymphoid malignancies. Anticancer mechanisms in this process rely on inhibition of DNA synthesis, induction of apoptosis , etc.

Specifications

Storage

Store at -20°C

Verschickt in

Ice chest + Ice pads

Dieses Produkt erfordert Kühlkettenversand. Grundversand und andere Economy-Optionen sind nicht verfügbar.

Namen und Kennungen

Molekulargewicht

228.20

Application Protocols

No validated immunoassay or imaging protocols are specified for this small molecule. For biochemical use, typical practices include:

• Preparing aqueous or DMSO stock solutions at known molarity using UV absorbance at 260 nm for quantitation (use literature extinction coefficients for dUrd; calibrate instrument accordingly).
• For enzyme assays (e.g., thymidine kinase or uracil-DNA glycosylase studies), dilute stocks into the reaction buffer immediately before use; include appropriate positive/negative controls and time-course sampling.

Item-specific recommended dilutions, controls, or instrument settings: Not specified for this item; refer to application notes in the literature or develop in-house SOPs.

Biological Roles

Literature perspective (biochemistry; no clinical claims):

• Metabolic role:
  • 2-Deoxyuridine (dUrd) is a deoxyribonucleoside comprising uracil and 2-deoxyribose. In cells, free dUrd can be salvaged by thymidine kinase to form dUMP, which is a central branch point en route to dTMP and dTTP via thymidylate synthase and thymidylate kinase.
• DNA occurrence and repair:
  • Uracil is generally excluded from DNA; however, deoxyuridine residues appear in DNA by misincorporation or by deamination of deoxycytidine. Base-excision repair enzymes (uracil-DNA glycosylases, e.g., UNG, SMUG1) recognize and remove uracil from DNA, initiating repair.
• Enzymology and pathway studies:
  • dUrd and its phosphorylated derivatives (dUMP, dUDP) are convenient substrates for in vitro assays of kinases, phosphatases, and polymerases. Isotopically labeled dUrd is used to trace nucleotide flux in one-carbon and pyrimidine pathways.
• Spectroscopic/analytical properties:
  • Like other pyrimidine nucleosides, dUrd absorbs UV around 260 nm; extinction coefficients are used in quantifying stocks and monitoring enzyme reactions (values depend on solvent and pH; consult literature for exact coefficients).
• Cellular handling:
  • Transport across membranes is mediated by equilibrative and concentrative nucleoside transporters in biological systems; in cell-free systems, uptake is irrelevant but stability considerations (pH, temperature) remain important.

Buffer Applications

This compound is not itself a buffering agent. It is typically dissolved in existing buffers for biochemical assays.

Practical guidance (general):

• Suitable buffers: PBS, Tris-HCl, HEPES, or phosphate buffers near neutral pH (6.8–8.0) to preserve the N-glycosidic bond.
• Preparation: dissolve the weighed solid in prewarmed buffer; filter through 0.22 μm if sterility is required. Avoid strong acids/bases which can cleave the glycosidic bond or modify the uracil ring.
• Typical working ranges: millimolar concentrations are common in enzymatic assays; determine concentration spectrophotometrically at 260 nm using a literature extinction coefficient for dUrd.

If a dedicated buffering function is required, select an appropriate buffer from Good’s buffers or phosphate systems; 2-deoxyuridine does not provide significant buffering capacity in the physiological pH range.

Green Alternatives

Because 2-deoxyuridine is not a process solvent but a polar substrate, “green” considerations focus on the media used to dissolve or transform it.

Greener media options (literature/general):

• Aqueous biocatalysis: many transformations on nucleosides (phosphorylation, transglycosylation by nucleoside phosphorylases) proceed efficiently in water or buffered water, minimizing VOC use.
• Water-miscible green co-solvents: glycerol, ethylene carbonate, propylene carbonate can sometimes replace DMF/DMSO for enzyme-compatible systems.
• Safer organics for protection chemistry:
  • Replace DMF with MeCN or 2-MeTHF when compatible with reagents (e.g., DMTr protection often tolerates MeCN/pyridine mixtures).
  • Use ethanol/water for workups and crystallizations in lieu of chlorinated solvents.

Trade-offs:

• High polarity demands highly polar solvents; greener choices can limit solubility or reaction rates.
• Some protecting-group steps (e.g., phosphitylation) require rigorously anhydrous, aprotic media where greener alternatives may be limited.

Mini-comparison (general guidance):

• DMSO vs MeCN: DMSO offers superior solubility but is harder to remove; MeCN is more volatile and widely accepted in green solvent guides.
• DMF vs Cyrene/PC: Cyrene or propylene carbonate may be viable for certain base-protection steps but can be more viscous and less established in nucleoside chemistry.

Pharmaceutical Uses

No pharmacopeial grade or excipient role is specified for this item; refer to CoA/Spec Sheet. The information below is general and intended for research/manufacturing development context only, without therapeutic claims.

General considerations (literature):

• Role in process development: native nucleosides like 2-deoxyuridine are used as reference standards, system suitability markers, and process controls in analytical methods supporting nucleotide/nucleoside manufacturing.
• Impurity/degradation studies: dUrd can arise as a process impurity or degradation product in nucleotide-based APIs; authentic material is used for method development and stress testing.
• Derivatization precursor: used to prepare protected phosphoramidites for solid-phase oligonucleotide synthesis (SPOC), relevant to manufacturing workflows of DNA-based research reagents.

Compliance notes:

• Any GMP use would require dedicated qualification (identity/purity, residual solvents, elemental impurities) and may demand compendial alignment where applicable. This listing is for research use only as stated in the Product Data.

Physical Properties

• Item-specific specifications (appearance, purity, water, metals, UV cutoff): Not specified for this item; refer to CoA/Spec Sheet.
• Storage: Store at −20 °C (per Product Data). Shipped cold (ice chest + ice pads).

Literature/general properties (for reference only; not item-specific specifications):

• Physical state: crystalline solid; colorless to off-white (literature, typical for nucleosides).
• Melting point: commonly reported around 160–165 °C (may show softening/decomposition depending on heating rate; literature).
• Solubility:
  • Water: readily soluble to moderately soluble; solubility increases with temperature; typical lab stocks are prepared in water or aqueous buffer (literature qualitative).
  • Polar organics: soluble in DMSO and DMF; limited in methanol/ethanol; practically insoluble in nonpolar solvents (literature qualitative).
• pKa: uracil ring N3 is weakly acidic (pKa ~9.2–9.6 for uridine; deoxy analogue similar; literature, approximate).
• LogP: very low (highly hydrophilic; literature qualitative).
• Optical activity: exhibits specific rotation due to chiral sugar (value varies with solvent and concentration; literature).
• Hygroscopicity: low to moderate; prolonged exposure to humid air can cause caking or slow hydrolysis under harsh conditions (general observation for nucleosides).

Quality and Grades

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.

Guidance for interpreting common grades (general information):

• Research grade nucleosides are typically suitable for biochemical assays, synthesis, and analytical method development. When low UV background is critical (e.g., HPLC reference standards), an HPLC or LC–MS grade may be preferred.
• For oligonucleotide synthesis, end users often require orthogonally protected derivatives (e.g., 5′-O-DMTr, 3′-O-phosphoramidite) with stringent control of moisture and trace amines; such specifications do not apply to this unprotected nucleoside unless explicitly stated in the CoA.
• Stabilizers: None indicated. Nucleosides are generally supplied without stabilizers; any additive would be declared on the CoA if present.
• Verification: Identity is commonly supported by 1H/13C NMR, HRMS, and HPLC purity. For this item, consult the Aladdin CoA for exact acceptance criteria, purity assay, and residual solvent profile.

Reaction and Applications

Key uses of 2-deoxyuridine span biochemical studies and nucleoside/nucleotide chemistry.

• Biochemical applications (literature):
  • Substrate or precursor in nucleotide metabolism studies: phosphorylation by thymidine kinase to dUMP; subsequent methylation to dTMP by thymidylate synthase in cell-free systems.
  • DNA repair research: dU residues arise by cytosine deamination; uracil-DNA glycosylases (e.g., UNG) excise dU—dU-containing oligos or solutions serve as controls or substrates in excision assays.
• Synthetic/chemical applications (literature):
  • Starting point for 5-substituted dU analogs (e.g., 5-iodo-, 5-bromo-, 5-azido-, 5-ethynyl-dU) prepared via electrophilic substitution or cross-coupling at C5 of a 5-halogenated intermediate.
  • Precursor to phosphoramidites for DNA synthesis after 5′-O-DMTr protection and 3′-O-phosphitylation.
  • Glycosylation studies: participates in N-glycosidic bond formation/cleavage under controlled acid catalysis, informing stability of DNA under stress.
• Analytical uses:
  • Calibration/retention markers in HPLC/LC–MS for nucleoside separations; reference for UV response at 260 nm.

Practical notes:

• Protect 5′-OH (DMTr) selectively in pyridine with catalytic DMAP; 3′-OH can be protected silyl (TBDMS) under imidazole/DMF conditions.
• For functionalization at C5, halogenation (NIS/NBS) on the nucleoside or on protected derivatives gives 5-halo-dU, enabling Suzuki/Sonogashira/CuAAC after further derivatization.

Reaction Conditions

General literature guidance for common transformations of 2-deoxyuridine (not item-specific specifications):

• 5′-O-DMTr protection:
  • Reagents: 4,4′-dimethoxytrityl chloride (DMTrCl), pyridine (dry), catalytic DMAP.
  • Conditions: 0–25 °C, 1–4 h, inert atmosphere recommended. Monitor by TLC/HPLC. Typical isolated yields: high (≥80%) after silica with EtOAc/hexanes + 1–2% TEA.
• 3′-O-silylation (TBDMS):
  • Reagents: TBDMS-Cl, imidazole, dry DMF.
  • Conditions: 20–40 °C, 4–16 h. Work up with aqueous NaHCO3; purify by column or crystallization. Typical yields: 70–90% (substrate-dependent).
• Phosphitylation (3′-O):
  • Reagents: 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, DIPEA, CH2Cl2/MeCN, 4 Å molecular sieves.
  • Conditions: 0–25 °C under dry argon; 0.5–2 h. Protect from moisture; quench with mild base. Typical yields: 60–85%.
• C5 halogenation:
  • Reagents: NIS or NBS, acetonitrile/DMF, sometimes with acid scavenger.
  • Conditions: 0–25 °C, 1–6 h. Affords 5-I or 5-Br derivatives; further cross-coupling under Pd catalysis (e.g., Pd(PPh3)4, base, toluene/Et3N or DMF) at 25–80 °C.
• Sonogashira on 5-iodo-dU (protected):
  • Reagents: Pd(PPh3)2Cl2/CuI, terminal alkyne, Et3N or i-Pr2NH, DMF or THF.
  • Conditions: 25–60 °C, 2–12 h. Typical yields: 60–85% after deprotection sequence.

Notes:

• Rigorous drying is crucial when handling phosphoramidites or moisture-sensitive steps.
• For aqueous enzymatic transformations (e.g., nucleoside phosphorylase), buffers at pH 7–8 and 25–40 °C are common; reaction times vary from 1–24 h depending on enzyme load.

Safety and Handling

• GHS classification, signal word, hazard statements, and pictograms: Not specified for this item; refer to the product SDS for authoritative safety information.
• General characteristics: 2-Deoxyuridine is a non-volatile, low-hazard nucleoside typically handled safely on the bench. Avoid inhalation of dust and contact with eyes/skin as with all fine organic powders.

Practical precautions (general laboratory guidance):

• Personal protective equipment: lab coat, safety glasses, and nitrile gloves.
• Engineering controls: handle powders in a clean, low-draft area or fume hood to minimize dust; use local exhaust ventilation during weighing.
• Incompatibilities: strong oxidizers, strong acids or bases under forcing conditions (may promote glycosidic bond cleavage or base degradation).
• Spill/cleanup: avoid creating dust; collect mechanically or with damp disposable wipes; dispose according to institutional and local regulations.
• First aid (overview; defer to SDS):
  • Inhalation: move to fresh air; seek medical advice if symptoms occur.
  • Skin/eyes: rinse with water for several minutes; remove contaminated clothing; obtain medical attention if irritation persists.
  • Ingestion: rinse mouth; do not induce vomiting; seek medical advice.
• Fire safety: organic solid; use water spray, CO2, dry chemical, or foam. Combustion may produce nitrogen/oxygen-containing irritants.
• Stability: stable as a dry solid when stored at −20 °C protected from moisture and light (per Product Data for storage; general chemistry knowledge for stability).

Solvent Selection

2-Deoxyuridine is a polar, hydrogen-bonding solid. Solvent choice is driven by solubility and downstream use (biochemical vs. synthetic).

• Polarity/miscibility (literature, general):
  • Highly polar and hydrophilic; dissolves well in water and in polar aprotics like DMSO and DMF. Limited solubility in lower alcohols; negligible in ethers and hydrocarbons.
• Typical selections by application:
  • Biochemical assays: water, PBS, Tris, or HEPES buffers (pH 6.8–8.0). Filter-sterilize and use fresh to minimize hydrolysis.
  • Stock solutions for cell-free enzymology: water or 1× buffer; if higher concentration is required, prepare a DMSO stock and dilute into aqueous media.
  • Organic synthesis: anhydrous DMF, DMSO, pyridine, or acetonitrile for protection/phosphitylation reactions; ensure rigorous drying to protect moisture-sensitive reagents.
• Practical tips:
  • Warm to 30–37 °C with gentle vortexing/sonication to accelerate dissolution in water.
  • Avoid strong acid in protic media (risk of N-glycosidic bond cleavage). Maintain near-neutral pH in aqueous solutions.
• Comparison (general):
  • Versus thymidine: similar solubility but slightly higher polarity due to the uracil carbonyl pattern; dissolution behavior in water is comparable.
  • Versus ribonucleosides: deoxy analogs are slightly less polar due to one fewer hydroxyl, sometimes improving solubility in polar organics.

Storage and Reconstitution

• Storage conditions (from Product Data): Store at −20 °C. Ship on ice (ice chest + ice pads). Keep container tightly closed, protected from moisture and light.
• Stability (general guidance): Dry solid is stable for extended periods at −20 °C. Aqueous solutions are best prepared fresh; at neutral pH and refrigerated (2–8 °C), short-term stability is typically acceptable. Avoid strong acid/base which can cleave the glycosidic bond.

Reconstitution and stock preparation (general):

• Solvents: water, buffer (e.g., PBS/Tris, pH ~7–8), or DMSO for high-concentration stocks.
• Technique: warm gently (30–37 °C) and vortex/sonicate to aid dissolution; filter-sterilize through 0.22 μm for sterile applications.
• Concentration verification: quantify by UV at 260 nm using an appropriate extinction coefficient for 2-deoxyuridine (literature value; verify in your matrix).
• Aliquoting: divide into single-use portions; store frozen (≤−20 °C) to minimize freeze–thaw. Label with solvent, concentration, and preparation date.
• Freeze–thaw: avoid repeated cycles; discard if precipitation, discoloration, or unexpected UV spectra are observed.

Any item-specific limits (e.g., water content, residual solvents, exact solubility) are Not specified for this item; refer to CoA/Spec Sheet.

Structure and Identity

A canonical pyrimidine 2′-deoxyribonucleoside consisting of uracil N1-glycosidically linked to 2-deoxy-D-ribofuranose.

• Item-specific identifiers from Product Data:
  • CAS: 21052-20-0
  • SKU: D1425542
  • Category: Small molecules and compound libraries (research use only)
• Literature/computed identifiers (general reference, not item-specific specs):
  • Common name: 2-Deoxyuridine (dUrd)
  • Synonyms: 1-(2-deoxy-β-D-ribofuranosyl)uracil; 2′-Deoxyuridine; dU
  • Molecular formula: C9H12N2O5 (literature)
  • Molecular weight: ~228.20 g/mol (literature)
  • SMILES (literature): Not specified for this item; refer to CoA/Spec Sheet or public databases.
  • InChIKey (literature): Not specified for this item; refer to CoA/Spec Sheet or public databases.
• Structural features (descriptive):
  • Pyrimidin-2,4-dione ring (uracil) with carbonyls at C2 and C4; double bonds at C5–C6.
  • N1-glycosidic linkage to a β-D-2-deoxyribofuranose; deoxygenated at the 2′ position (–H in place of ribose 2′-OH).
  • Sugar stereochemistry typical of natural nucleosides: 1′β configuration, with free 3′-OH and 5′-OH functional handles.
  • No chiral centers in the base; multiple stereocenters in the sugar (D-configuration). 2D depiction would show the uracil ring planar and the furanose ring in an envelope conformation linked at N1–C1′.

Synthetic Utility

As a bifunctional scaffold with a reactive pyrimidine ring and two free sugar hydroxyls, 2-deoxyuridine is a versatile building block.

Key transformations (literature):

• Hydroxyl protection:
  • 5′-O-DMTr installation (DMTrCl, pyridine, catalytic DMAP) for oligo synthesis precursors.
  • 3′-O-silylation (TBDMS-Cl, imidazole, DMF) or acylation for orthogonal protection.
• Phosphitylation:
  • 3′-O or 5′-O conversion to 2-cyanoethyl N,N-diisopropylphosphoramidites (using Cl–P(NiPr2)(OCH2CH2CN), DIPEA, CH2Cl2/MeCN) enabling automated DNA synthesis.
• C5 functionalization of the uracil ring:
  • Halogenation (NIS/NBS) to 5-iodo/bromo-dU; subsequent cross-couplings (Suzuki, Sonogashira, Stille) furnish 5-aryl/alkynyl analogs.
  • Electrophilic substitution to 5-nitrated intermediates followed by reduction or further elaboration.
• Click handles:
  • Introduction of azido- or ethynyl groups at C5 (e.g., from 5-iodo-dU via CuAAC/Sonogashira) for bioconjugation.
• Glycosyl chemistry:
  • Formation/cleavage of the N-glycosidic bond used to prepare labeled or modified sugars; Vorbrüggen-type glycosylation of silylated uracils with activated deoxyribose donors (literature conditions).

Utility highlights:

• Orthogonal protection strategies allow regioselective elaboration at sugar OH groups while maintaining base integrity.
• The mild reactivity of the uracil ring (vs. cytosine) simplifies selective C5 derivatization without exocyclic amines.

Target Specificity

Not applicable to this product type. 2-Deoxyuridine is a small-molecule nucleoside, not an antibody or affinity reagent. No clone, isotype, antigen, or species reactivity data apply.