This compound belongs to the class of organic compounds known as pyrimidine nucleosides. These are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
External Descriptors
Not available
1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.
Zertifikate (CoA, COO, BSE/TSE und Analyse-Diagramm)
C of A & Other Certificates(BSE/TSE, COO):
Analytical Chart:
Chemische und physikalische Eigenschaften
Molekulargewicht
284.260 g/mol
XLogP3
-1.200
Hydrogen Bond Donor Count
3
Hydrogen Bond Acceptor Count
6
Rotatable Bond Count
4
Exact Mass
284.101 Da
Monoisotopic Mass
284.101 Da
Topological Polar Surface Area
111.000 Ų
Heavy Atom Count
20
Formal Charge
0
Complexity
451.000
Isotope Atom Count
0
Defined Atom Stereocenter Count
4
Undefined Atom Stereocenter Count
0
Defined Bond Stereocenter Count
0
Undefined Bond Stereocenter Count
0
The total count of all stereochemical bonds
0
Covalently-Bonded Unit Count
1
Lösungsrechner
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Application Protocols
Item-specific, validated protocols are not provided for this product. The following general workflows illustrate typical research uses of N(3)-Allyluridine; adjust to your system and verify experimentally.
Preparation of stock solutions (general):
Dissolve in anhydrous DMSO to 10–50 mM; vortex and sonicate gently if needed. Filter (0.22 µm) for cell-free assays or chemical transformations. Store small aliquots to minimize freeze–thaw.
Pd-catalyzed deallylation (bench-scale):
Charge a dry flask with N(3)-Allyluridine (1.0 equiv) and THF/MeOH (0.05–0.1 M). Add Pd(PPh3)4 (0.02–0.05 equiv) and morpholine (2–3 equiv). Stir at 25–35 °C under N2, monitoring by HPLC. Upon completion, filter through a metal scavenger pad and purify by reversed-phase chromatography.
Thiol–ene tagging (analytical labeling):
Dissolve substrate in degassed MeOH or DMF (0.05 M). Add 1.2 equiv thiol label and a photoinitiator. Irradiate at 365–405 nm for 10–30 min while cooling. Quench with antioxidant (e.g., BHT), then analyze by LC-MS.
These are illustrative literature-style procedures, not product specifications. Always perform small-scale trials and consult the SDS and CoA for safety and quality parameters.
Biological Roles
Item-specific biological/clinical data are not provided. The following is general context about uridine analogs and N3 substitution.
Uridine in biology (reference): Uridine is a ribonucleoside component of RNA, participating in base pairing (U–A) and numerous post-transcriptional modifications. It contributes to RNA structure, catalysis (ribozymes), and recognition by proteins and enzymes.
Impact of N3 substitution: The N3 position of uracil participates in hydrogen bonding. N3-allylation blocks the N3–H, disrupting canonical Watson–Crick pairing and altering base pKa and H-bonding patterns (literature). This can modulate duplex stability and enzyme recognition.
Tool compound concept: N(3)-Allyluridine can serve as a chemical biology handle—the allyl group is amenable to post-synthetic modification (e.g., thiol–ene) allowing attachment of probes, fluorophores, or affinity tags to RNA or nucleoside derivatives for mechanistic studies.
Enzymatic incorporation (general): Some polymerases tolerate N3-modified uridine triphosphates to varying degrees; however, tolerance is sequence- and enzyme-dependent. The nucleoside itself requires phosphorylation to enter nucleotide metabolism; no item-specific biochemical data are provided.
Research use only: Per product data, this material is supplied strictly for research and laboratory applications. It is not intended for diagnostic, therapeutic, or other clinical uses.
Buffer Applications
This product is a nucleoside building block rather than a buffering agent. It is not typically used to establish or maintain pH in biochemical assays.
Practical notes (general):
For dissolving or handling N(3)-Allyluridine in biological experiments, choose neutral to slightly basic buffers (e.g., phosphate, HEPES, Tris at pH 7.0–8.0) to limit acid- or base-catalyzed degradation of the ribose or glycosidic linkage.
When performing metal-catalyzed post-functionalizations in aqueous media, avoid buffers that strongly chelate metals (e.g., high EDTA) unless deallylation or metathesis chemistry is complete; adjust ionic strength to support solubility.
No item-specific buffer compatibility or recipe data are provided; consult your application requirements and perform small-scale solubility/stability checks.
Green Alternatives
Greener process design for N(3)-Allyluridine work should focus on solvent selection, catalyst loading, and minimizing protecting-group manipulations.
Opportunities (general/literature):
Solvent substitution:
Replace high-toxicity dipolar aprotics (DMF, NMP) with green polar solvents like 2-methyltetrahydrofuran (2-MeTHF) for workups or propylene carbonate for some coupling steps, provided solubility is adequate.
For analytical/sample prep, use water–ethanol mixtures where feasible instead of pure acetonitrile.
Catalysis efficiency:
In Pd-catalyzed deallylation, employ ppm–level Pd in water/ethanol with benign nucleophiles (e.g., morpholine) and efficient Pd scavengers to reduce metal waste.
For thiol–ene functionalizations, visible-light photoredox with organic photocatalysts reduces reliance on heavy metals.
Process intensification:
Microwave or flow conditions can shorten reaction times and reduce solvent/catalyst usage for derivatization steps.
Comparison snapshot (general):
DMF vs. 2-MeTHF: DMF offers superior solvation and is common for nucleosides; 2-MeTHF is bio-based and lower toxicity but may require co-solvents to dissolve highly polar substrates.
DCM vs. EtOAc: DCM is effective but chlorinated; ethyl acetate is a greener alternative for extractions and some chromatographic separations.
Note: Green alternatives must be verified experimentally for solubility/reactivity with this substrate. No item-specific solvent compatibility or stability data are provided here.
Pharmaceutical Uses
No pharmacopeial status, excipient role, or formulation grade is specified for this product; refer to the CoA/Spec Sheet.
General context (research/manufacturing only; no clinical claims):
Intermediate for nucleoside/nucleotide chemistry: N(3)-Allyluridine can serve as a synthetic intermediate toward modified nucleotides or prodrugs where N3 protection and/or an allyl handle is advantageous.
Conjugation handle: The allyl group enables attachment of reporter groups or delivery vectors, useful in preclinical assay development and biomolecular conjugates.
Deprotection strategy: The N-allyl group is removable under mild Pd(0) conditions, which can be attractive for late-stage deprotection in complex molecules sensitive to acid/base.
Quality and regulatory note:
Material is supplied for research use only (per product data). It is not intended for use in humans or for clinical applications. Any scale-up or use in regulated settings requires appropriate qualification, impurity profiling, and validation outside the scope of this listing.
Physical Properties
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Weight (item-specific): Not specified for this item; refer to CoA/Spec Sheet. (Literature estimate ~284.27 g/mol noted in Structure & Identity.)
Molecular Formula (item-specific): Not specified for this item; refer to CoA/Spec Sheet. (Literature: C12H16N2O6.)
Melting point, boiling point, density, refractive index: Not specified for this item; refer to CoA/Spec Sheet.
General/literature guidance for nucleoside analogs like N3-allyluridine (not item specifications):
Physical state: Typically a crystalline solid; polymorphism and solvate formation are possible for ribonucleosides.
Solubility (qualitative): Moderately to highly soluble in polar aprotic solvents (DMSO, DMF). Aqueous solubility may be lower than uridine due to the hydrophobic allyl substituent, but can often be improved by gentle warming (30–40 °C) or pH adjustment (slightly basic conditions enhance solubility via deprotonation of ribose hydroxyls is minimal; N3 is substituted and not ionizable).
LogP/logD (trend): Expected to be higher than uridine because of the allyl group; still overall polar due to multiple hydroxyls and carbonyls (literature trend for N-alkylated uridines).
pKa: The uracil N3 proton is replaced; remaining acidic/basic sites are weakly ionizable (literature pKa for uridine N3 ~9.2 when protonated; not applicable here due to N3-allylation).
Always consult the CoA/Spec Sheet for definitive item-specific physicochemical data and the SDS for handling limits.
Quality and Grades
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Guidance on interpreting grades (general):
Research grade: Typical for screening libraries and building blocks; suitable for most synthesis and discovery workflows. Purity often verified by HPLC/LC-MS and NMR.
HPLC grade/LC-MS suitability: Indicates low nonvolatile residue and controlled UV background—useful for chromatographic methods. For nucleosides, low baseline absorbance at 260 nm is helpful in analytical QC.
Biochemical grade: May imply tighter control of metal ions, endotoxin, and bioburden—relevant if using polymerases or enzymes that are metal-sensitive.
Verification practices (recommended):
Request or consult the Certificate of Analysis (CoA) for the specific lot to view exact purity assay, residual solvent limits, and analytical methods (HPLC area%, NMR, MS).
If performing sensitive transformations (e.g., Pd-catalyzed deallylation), consider trace metal content and run a small test reaction to confirm performance.
For oligonucleotide applications, confirm nucleobase integrity (uracil carbonyl signals) and the allyl substitution (vinylic protons in 1H NMR ~5.0–6.0 ppm; literature guidance) before scale-up.
Stabilizers/additives:
None stated for this item. If stabilizers or salt forms are relevant, they will be listed on the CoA/Spec Sheet; absence here does not imply presence or absence in the product.
Reaction and Applications
N(3)-Allyluridine is a versatile nucleoside analog where the N3 position of uracil carries an allyl group. This handle both blocks Watson–Crick hydrogen bonding at N3 and provides a reactive alkene for downstream transformations.
Representative applications (literature/general):
Protecting/temporary masking group at N3: Employed to control base pairing or regiochemistry during nucleoside synthesis and oligonucleotide assembly; subsequently deprotected by Pd-catalyzed deallylation (Tsuji–Trost type) to regenerate uridine under mild conditions.
Chemical biology probes: N3-substituted uridines can be incorporated into RNA by solid-phase synthesis or enzymatic polymerases (polymerase tolerance varies by substitution). Post-incorporation, the allyl can be modified (e.g., thiol–ene additions, cross-metathesis) to introduce tags.
Cross-metathesis/olefin chemistry: The terminal alkene enables olefin cross-metathesis (Grubbs/Hoveyda catalysts) with suitably functionalized partners to append affinity labels or crosslinkers to the nucleobase.
Palladium-mediated transformations: Beyond deprotection, N-allyl groups can participate in allylic substitution chemistry under Pd(0) catalysis with soft nucleophiles, enabling diversification at N3 (with caution to avoid glycosidic bond cleavage).
Materials/nanotechnology contexts: Allyl-bearing nucleosides can be used to assemble functional nucleic acids or polymer–nucleoside conjugates via radical polymerizations or click-like alkene reactions.
Practical considerations:
Maintain neutral to slightly basic conditions to preserve ribose integrity; limit exposure to strong acids/bases and extended heating.
For post-functionalization on RNA, ensure metal catalyst and ligand systems are compatible with aqueous media and minimize strand scission (use scavengers and brief reaction times).
Reaction Conditions
The following are literature-style, general reaction conditions relevant to N-allyl nucleosides; they are guidance only and not item specifications.
Pd-catalyzed deallylation (Tsuji–Trost type):
Catalyst: Pd(PPh3)4 (1–5 mol%) or Pd2(dba)3/PPh3; solvent: THF, DMF, or MeOH; additive/nucleophile: morpholine, dimedone, or similar soft nucleophiles (2–5 equiv).
Temperature: 20–40 °C; time: 0.5–6 h; atmosphere: N2/Ar. Workup with aqueous quench and metal scavenging.
Aqueous variant: H2O/EtOH with catalytic Pd(0) and phosphate buffer can be effective; minimize exposure of ribose to base.
Thiol–ene modification of allyl:
Initiation: AIBN (thermal, 60–80 °C) in polar aprotics, or photoinitiated under 365–450 nm with organic photoinitiators.
Typical stoichiometry: 1.0–1.5 equiv thiol; monitor by LC-MS/UPLC at 260 nm.
Olefin cross-metathesis:
Catalyst: Grubbs II or Hoveyda–Grubbs II (2–10 mol%); solvent: DCM, toluene, or green alternatives (EtOAc, 2-MeTHF) if soluble.
Conditions: 25–50 °C, 1–12 h; ethylene purge for ethenolysis variants.
Epoxidation/hydroxylation of allyl:
mCPBA (epoxidation) or OsO4/NMO (dihydroxylation) under mild conditions; protect ribose diols as needed to avoid side reactions.
Analytical control:
Monitor reactions by HPLC at 260 nm and confirm identity by HRMS and 1H/13C NMR (allyl vinylic protons ~5.0–6.0 ppm; disappearance upon deallylation).
Note: Optimize solvent choice to balance solubility with green chemistry goals; ensure thorough removal of heavy metals after catalysis.
Safety and Handling
GHS classification, signal word, pictograms, H-statements: Not specified for this item; refer to the SDS for authoritative safety information.
General hazards (literature/general): Nucleoside analog solids are typically of low volatility and low acute toxicity but may cause irritation to skin, eyes, and respiratory tract upon exposure to dust.
PPE recommendations: Wear lab coat, safety glasses or splash goggles, and appropriate chemical-resistant gloves (e.g., nitrile). Use a dust mask or handle in a fume hood if powder becomes airborne.
Handling notes:
Avoid generating dust; transfer using spatulas and weigh boats in a controlled environment.
Protect from moisture; hygroscopic uptake can alter mass readings and solution concentrations.
Avoid contact with strong oxidizers and strong acids/bases that could degrade the ribose or uracil moieties.
First aid (overview; defer to SDS):
Skin contact: Wash with soap and water; remove contaminated clothing.
Eye contact: Rinse cautiously with water for several minutes; seek medical attention if irritation persists.
Inhalation: Move to fresh air; obtain medical advice if symptoms occur.
Ingestion: Rinse mouth; do not induce vomiting; seek medical advice.
Spill management: Gently collect solids to avoid dust; wipe area with damp disposable towels. Dispose of waste per institutional and local regulations.
Fire safety: Combustible organic solid; use water spray, CO2, dry chemical, or foam. Thermal decomposition may produce CO/CO2 and nitrogen oxides.
Always consult the SDS supplied with the lot for specific hazard and emergency response details.
Solvent Selection
As an N-allylated ribonucleoside, N(3)-Allyluridine is polar and hydrogen-bonding, favoring polar protic and aprotic media.
Primary dissolution choices (general guidance):
DMSO: Excellent solvating power for nucleosides; commonly used for stock solutions and screening libraries.
DMF/NMP: Useful for synthesis and coupling chemistry; good for deallylation pre-mixes and derivatizations.
Water/aqueous buffer: Solubility may be moderate; gentle warming (30–40 °C) and pH 7–8 can improve dissolution without base-promoted degradation.
Alcohols (MeOH, EtOH): Intermediate solubility and convenient for workups/crystallizations.
Less suitable: Nonpolar solvents (hexanes, toluene) generally exhibit poor solubility due to multiple hydroxyls and carbonyls.
Polarity comparisons (literature/general):
Uridine analogs typically show higher solubility in DMSO > DMF ≈ water (warm) > MeOH/EtOH >> acetonitrile >> ethers.
Practical tips:
Filter stocks (0.22 µm) if particulate persists; avoid strong base during dissolution, as ribose acetalization/elimination can occur under harsh basic conditions.
For moisture-sensitive coupling or metal-catalyzed steps, dry solvents (Karl Fischer–controlled) are recommended; although no item-specific water limit is provided, solvent dryness strongly impacts nucleoside derivatization yields.
Note: No item-specific solubility parameters are provided; consult the CoA/Spec Sheet for lot-specific guidance.
Shipped in: Not specified for this item; refer to CoA/Spec Sheet.
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
General guidance (not item-specific specifications):
Store tightly sealed in a dry, inert atmosphere (desiccator with desiccant) to minimize moisture uptake. Protect from prolonged light exposure to avoid potential allyl oxidation.
If long-term storage is planned, consider 2–8 °C as a precaution to slow degradation, unless hygroscopic behavior or crystallization from mother liquors suggests otherwise.
Reconstitution tips:
For chemical workflows, prepare concentrated stocks in anhydrous DMSO or DMF. For biochemical assays, dissolve in warm aqueous buffer or water with a small percentage of DMSO if needed to aid solubility.
Filter solutions (0.22 µm) for sensitive assays; use freshly prepared solutions when performing metal-catalyzed reactions to minimize peroxide or oxygen effects.
Avoid repeated freeze–thaw cycles; aliquot stocks into single-use vials and store at the recommended temperature.
Stability testing:
Verify integrity by HPLC (UV 260 nm) and 1H NMR after storage. Watch for loss of allyl signals or glycosidic cleavage products.
Note: Follow the lot-specific CoA/Spec Sheet for any additional storage, stability, or reconstitution instructions.
Structure and Identity
A nucleoside analog derived from uridine bearing an allyl substituent at the N3 position of the uracil base.
Product Name (catalog): N(3)-Allyluridine (SKU: N976602)
CAS: 103951-13-9 (product data)
PubChem CID: 128450 (product data)
InChIKey: 368788 (product data; note: format appears abbreviated relative to typical InChIKeys)
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
Molecular Formula: C12H16N2O6 (literature for N3-allyluridine, derived from uridine + allyl at N3)
Base: Uracil (pyrimidine-2,4-dione) with an N3-allyl substitution (–CH2–CH=CH2) replacing the N3–H.
Sugar: β-D-ribofuranose linked via an N1–C1′ glycosidic bond, bearing 3′,5′-diol and 2′-hydroxyl groups typical of ribonucleosides.
Functional groups: Two amide carbonyls on the uracil ring, multiple alcohols on ribose, and a terminal alkene within the allyl group.
Stereochemistry: Ribose centers typically at 1′R,2′R,3′R,4′R (literature, as in uridine); no additional stereocenters introduced by N3-allylation.
2D structure in words (general): uracil ring (positions 2,4 = carbonyls; 1 = glycosidic to ribose; 3 = allyl-substituted; 5/6 = vinylic CH) attached to a five-membered ribofuranose ring bearing three vicinal hydroxyls. The allyl substituent projects from N3 providing a terminal C=C handle for further transformation.
Synthetic Utility
Key aspects that make N(3)-Allyluridine valuable in synthesis (literature/general):
Protected nucleobase: N3-allylation masks a key H-bonding site, steering regioselectivity during further functionalization of the nucleobase and minimizing undesired reactions at N3 during ribose or base derivatization.
Allyl as a traceless protecting group: Deprotect via Tsuji–Trost deallylation (Pd(0), soft nucleophile) to restore uridine—useful when acid- or base-labile groups are present elsewhere.
Orthogonal handle: The terminal alkene supports late-stage diversification (thiol–ene additions, epoxidation, dihydroxylation, cross-metathesis), enabling libraries of modified uridines/RNAs.
Compatibility: Under carefully controlled conditions, N-allyl protection is compatible with glycosylation, silyl protection of ribose hydroxyls (e.g., TBDMS/TBS), and phosphoramidite chemistry.
Retrosynthetic value: Provides a convergent route where base protection and derivatization can be decoupled from sugar manipulations; after elaboration, the allyl can be removed to reveal the native base.
Considerations:
Avoid strong acids/bases and extended high-temperature steps that risk glycosidic bond cleavage.
Monitor for potential O- vs N-allyl migration under strongly basic or metal-catalyzed conditions; select ligands/nucleophiles that favor clean N–C3 deallylation when desired.
Trace Pd removal (silica–thiol, metal scavengers) is recommended post-deallylation to meet analytical purity targets, especially for enzyme-facing applications.
Target Specificity
Not applicable. This product is a small-molecule nucleoside building block, not an antibody, enzyme, or affinity reagent. No antigen, epitope, clone, or species reactivity information applies.
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