2'-Deoxy-2'-fluorocytidine - Moligand™, 10 mM in Water , CAS No.10212-20-1

CAS: 10212-20-1 Cat. No.: D1500423 Summenformel: C₉H₁₂FN₃O₄ Molekulargewicht: 245.21 EG-Nummer: 190-339-1

GRADE & PURITY Moligand™, 10 mM in Water

Storage

Protected from light,Store at -80°C

Shipped In

Dry ice packs + Cold packs

Übersicht

2'-Deoxy-2'-fluorocytidine, an nucleoside analog, is a potent inhibitor of Crimean-Congo hemorrhagic fever virus (CCHFV) replication. 2′-deoxy-2′-fluorocytidine can act synergistically with T705 to increase the potency of both compounds antiviral effects on CCHFV replication.

Specifications

Spezifikationen & Reinheit

Moligand™, 10 mM in Water

Storage

Protected from light,Store at -80°C

Verschickt in

Dry ice packs + Cold packs

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

Note

Moligand™

Aktionsart

INHIBITOR

Namen und Kennungen

Isomere SMILES

C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)F

WGK Deutschland

3

Molekulargewicht

245.21

Reaxy-Rn

24724908

Reaxys-RN_link_address

https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=24724908&ln=

Chemische und physikalische Eigenschaften

• Spezifische Drehung [α]: 80° (C=1,MeOH)
• Schmelzpunkt (°C): 167°C(lit.)

Application Protocols

No vendor-tested biological assay protocols are provided for this item.

• General guidance (non-binding; literature-based)
  • Stock preparation: Dissolve in nuclease-free water or DMSO to 10–100 mM; filter sterilize (0.22 µm) if using in biochemical assays.
  • Enzymatic assays: Prepare reaction mixes with Mg2+ (1–10 mM) in Tris/HEPES buffer, pH 7–8. Include appropriate controls (deoxycytidine vs 2'-deoxy-2'-fluorocytidine) to assess enzyme selectivity.
  • Storage of stocks: Aliquot to minimize freeze-thaw; keep protected from light.

For application-specific, validated protocols, consult primary literature or develop in-house SOPs.

Biological Roles

• Nature of the compound (literature/general)
  • 2'-Deoxy-2'-fluorocytidine is an analog of 2'-deoxycytidine in which fluorine replaces hydrogen at the 2' position of the deoxyribose. The cytosine base retains its standard Watson–Crick hydrogen-bonding face.
• Biophysical/biochemical implications
  • The 2'-F substituent is small and highly electronegative, biasing the sugar toward a C3'-endo (north) pucker relative to deoxycytidine. This can modulate duplex geometry and thermal stability in DNA and DNA/RNA hybrids (literature, general).
  • As a deoxynucleoside, it can be phosphorylated in vitro to nucleotides (FdCMP/FdCDP/FdCTP), which are substrates or inhibitors for certain DNA polymerases and kinases in biochemical studies (no clinical claims).
  • Fluorination increases resistance to some glycosidic bond cleavage pathways and can affect susceptibility to deamination compared with unmodified deoxycytidine (literature trends; exact rates are enzyme/pH dependent).
• Research uses (non-clinical)
  • Tool compound for probing polymerase selectivity, fidelity, and processivity with modified 2'-substituted deoxynucleotides.
  • Component in modified DNA or chimeric oligonucleotides to investigate structure–activity relationships in nucleic acid recognition and nuclease resistance.
  • Analytical calibrant for fluorinated nucleoside detection/quantitation by LC–MS.
• Metabolism note
  • In cell-free systems, nucleoside kinases and deaminases can act on cytidine analogs with altered efficiencies; 2'-F substitution modulates these interactions (literature, general). Exact kinetic parameters are context-specific.

Buffer Applications

This compound is not a buffering agent and is not typically used to prepare buffer systems.

• Practical note (general)
  • When preparing aqueous solutions for biochemical assays, dissolve in nuclease-free water or neutral buffers (e.g., 10 mM HEPES or phosphate, pH ~7.2) only if compatible with your assay. Avoid strongly basic buffers that can promote nucleoside degradation. Filter sterilize when sterility is required.

Green Alternatives

Because this product is a solid nucleoside analog rather than a process solvent, “green alternatives” pertain to selecting greener media for handling and synthesis.

• Greener solvent choices (general guidance)

  • Aqueous media: Favor nuclease-free water or buffered aqueous-organic mixtures for biochemistry and analytics when stability allows.
  • Alcohols (EtOH) vs MeCN/DCM: Prefer ethanol or isopropanol for crystallization/workup when compatible, reducing chlorinated solvent use.
  • 2-MeTHF/CPME vs THF/Et2O: For moisture-sensitive steps like phosphitylation, 2-MeTHF or CPME can sometimes replace THF/ethers, offering lower peroxide risk and improved sustainability.

• Tradeoffs (literature/general)

  • Acetonitrile is standard in phosphoramidite chemistry due to solvation and volatility; greener substitutes may impact coupling efficiency and require re-optimization of activators and bases.
  • Aqueous systems minimize VOCs but can accelerate hydrolysis/deamination of nucleosides at non-neutral pH or elevated temperatures.

• Example comparison (general)

  • Acetonitrile: High coupling efficiency; petrochemical origin; toxicity concerns.
  • Ethanol/water: Benign, low toxicity; may not dissolve protected intermediates; slower reactions possible.
  • 2-MeTHF: Bio-derived, lower miscibility with water; may require different drying protocols and activator selection.

• Practical steps

  • Use minimal solvent volumes, recycle solvents where feasible, and run at ambient temperature when compatible to reduce energy use.

Pharmaceutical Uses

No excipient or pharmacopeial status is provided for this item; it is sold for research use only.

• General formulation/manufacturing context (non-clinical)

  • Can serve as a synthetic intermediate or reference standard in the development of fluorinated nucleoside derivatives.
  • Phosphate prodrug strategies (e.g., aryl or amino acid phosphoramidates) are commonly explored on nucleoside scaffolds for permeability/stability optimization in medicinal chemistry research; suitability and protection schemes must be determined experimentally.
  • For analytical development, may be used to establish impurity/degradation profiles and retention times for related nucleosides in QC methods (HPLC/LC–MS).

• Compliance note

  • No claims of GMP manufacture, compendial compliance, or clinical use. For any regulated application, qualified material and documentation are required.

Physical Properties

• Item-specific specifications
  • Appearance: Not specified for this item; refer to CoA/Spec Sheet.
• Literature/general values and notes (for guidance only; not item specifications)
  • Physical state: Typically a white to off-white crystalline solid (literature, nucleoside analogs).
  • Molecular weight: ~245.21 g/mol (from formula C9H12FN3O4, literature calculation).
  • Solubility: Expected high solubility in water and polar protic/aprotic solvents such as water, methanol, and DMSO; limited solubility in nonpolar solvents (literature, nucleoside behavior).
  • pKa: Cytosine N3 has a basicity that gives typical nucleobase pKa values around 4.5 (protonation) and exocyclic amine basicity near 12–13 for deprotonation contexts; exact values for this analog are not widely tabulated (literature, approximate ranges only).
  • logP/logD: Nucleosides typically have very low logP (<0) at neutral pH due to multiple hydrogen-bond donors/acceptors; 2'-F may slightly increase lipophilicity versus deoxycytidine but remains polar (literature, qualitative).
  • Melting point, boiling point, density, refractive index, UV cutoff: Not specified for this item; refer to CoA/Spec Sheet.
• Practical handling implications (general)
  • Hygroscopicity: Nucleosides can absorb moisture; store tightly closed and desiccated.
  • UV absorbance: Cytidine chromophore absorbs near 270–280 nm; 2'-F substitution minimally perturbs base chromophore (literature, qualitative).

Quality and Grades

• Item-specific
  • Grade: Moligand™ — Aladdin Scientific’s small-molecule/compound library quality suitable for screening, hit validation, and exploratory synthesis.
• What Moligand™ implies (general explanation)
  • Intended for research use only; not for human or veterinary use.
  • Emphasis on identity confirmation and suitable purity for biochemical/chemical screening. Low levels of residual solvents and inorganic impurities are targeted, but exact specifications are batch-dependent.
  • UV/LC suitability: While nucleosides are readily monitored by UV around 270–280 nm, specific UV cutoff, residual solvent limits, or metal content for this item are Not specified for this item; refer to CoA/Spec Sheet.
• Verification & documentation
  • Typical characterization for nucleosides includes 1H/13C NMR, HRMS/ESI-MS, and HPLC purity; exact methods and acceptance criteria for this SKU are Not specified for this item; refer to CoA/Spec Sheet.
• Stabilizers/additives
  • No stabilizer information provided for this item. If stabilizers or special counter-ions are present, they will be listed on the CoA/Spec Sheet.

Reaction and Applications

• Research/manufacturer context
  • Listed under small molecules/compound library; suitable for screening, nucleoside chemistry, and as a reference standard for analytical methods. No specific manufacturer applications were provided beyond research use.
• Typical applications (literature/general)
  • Nucleotide synthesis: Chemical or enzymatic phosphorylation to mono-, di-, and triphosphates (FdCMP/FdCDP/FdCTP) for polymerase incorporation studies.
  • Oligonucleotide chemistry: Precursor to 3'-O- or 5'-O-phosphoramidites for solid-phase DNA synthesis to introduce 2'-F modifications into deoxy backbones; 2'-F can modulate duplex stability and nuclease resistance.
  • Medicinal chemistry building block: Scaffold for prodrug elaboration (e.g., phosphoramidate/ester masking of phosphate), without implying therapeutic claims.
  • Biophysical probes: Studying effects of 2'-substitution on sugar pucker (C3'-endo bias) and DNA/RNA hybridization thermodynamics.
• Analytical uses
  • Reference standard in LC–MS method development for fluorinated nucleosides; stable isotope-labeled internal standards may be paired where needed.
• Practical notes
  • Protect 3'/5' hydroxyls during selective conversions; common protections include silyl ethers (TBDMS) or cyclic acetals.
  • Avoid strong bases/acids that can promote N-glycosidic bond cleavage or base deamination. Maintain anhydrous conditions for phosphitylation and acylation steps.
  • For enzymatic phosphorylation, use kinase systems optimized for cytidine analogs; magnesium as cofactor and pH 7–8 are typical (literature).

Reaction Conditions

All guidance below is literature/general and must be optimized for your system; it is not a specification for this item.

• Phosphoramidite formation (5'-O)
  • Solvent: Anhydrous acetonitrile or dichloromethane.
  • Base: DIPEA or pyridine (2–4 equiv).
  • Reagent: 2-cyanoethyl N,N-diisopropylchlorophosphoramidite (1.2–1.5 equiv).
  • Temperature: 0–25°C; typically 1–3 h under inert atmosphere.
  • Workup: Quench with saturated NaHCO3, extract, and purify by silica with base-modified eluent.
• 5'-Monophosphate (chemical phosphorylation)
  • Reagents: POCl3 (limiting) in trimethyl phosphate at 0–5°C; quench into aqueous buffer then neutralize (literature for nucleosides).
  • Follow-up: Convert to di-/triphosphates with pyrophosphate salts (e.g., tributylammonium pyrophosphate) in DMF with Mg2+ or via phosphorimidazolidate routes.
• Enzymatic phosphorylation
  • Kinases: Deoxycytidine kinase systems in buffered aqueous solutions (pH 7–8), Mg2+ 5–10 mM, 25–37°C; times 0.5–6 h depending on enzyme loading and acceptance of 2'-F analogs.
• Protecting group manipulations
  • Silylation: Imidazole-catalyzed TBDMS-Cl in DMF; 0–25°C, 2–6 h (regioselectivity depends on solvent/base).
  • N4-acylation: Benzoyl chloride or acetic anhydride in pyridine; 0–25°C, 1–3 h.
• Analytical monitoring
  • LC–MS with aqueous MeOH/MeCN and volatile buffers (e.g., 10 mM ammonium formate, pH ~4.5–6.5) tracks mass and purity without derivatization.

Safety and Handling

• Item-specific hazard statements (from Product Data)
  • Signal word: Not specified for this item; refer to SDS.
  • H-statements: Not specified for this item; refer to SDS.
  • GHS classification and pictograms: Not specified for this item; refer to SDS.
• General laboratory safety (defer to SDS for authoritative guidance)
  • PPE: Wear lab coat, safety glasses, and appropriate chemical-resistant gloves. Use in a fume hood or well-ventilated area to avoid dust/aerosol inhalation.
  • Avoid contact with skin, eyes, and clothing. Wash hands thoroughly after handling.
  • Incompatibilities: Strong oxidizers and strong acids/bases may degrade nucleosides; avoid moisture for long-term storage.
  • First aid overview: If inhaled, move to fresh air; if on skin/eyes, rinse with water for ≥15 minutes; if ingested, rinse mouth. Seek medical attention per SDS.
  • Spill response: Avoid raising dust; collect with inert absorbent, transfer to a suitable waste container. Decontaminate area with water/ethanol.
• Special risks/notes (general)
  • Dust formation: Handle powders gently to minimize dust. Use antistatic and localized extraction if necessary.
  • Environmental: Avoid release to the environment; dispose of contents/container in accordance with local regulations.
  • Stability: Protect from light; maintain cold chain to minimize hydrolysis/deamination during storage (aligned with Product Data storage guidance).

Solvent Selection

• Polarity and solubility profile (literature/general)
  • 2'-Deoxy-2'-fluorocytidine is a highly polar, hydrogen-bonding nucleoside analog. It is typically soluble in water, aqueous buffers (pH-dependent), methanol, ethanol, and DMSO; poorly soluble in nonpolar media (hexanes, toluene).
  • For stock solutions in screening: DMSO or water (nuclease-free) are common. DMSO enhances stability during repeated freeze-thaw if aliquoted.
• Choosing solvents by application
  • Biochemical assays/polymerase studies: Nuclease-free water or low-ionic-strength buffers to avoid salt effects; adjust pH 6.5–7.5 to maintain base in unprotonated state.
  • Organic synthesis (protection/phosphitylation): Anhydrous acetonitrile, dichloromethane, or THF with base (e.g., DIPEA) under moisture-free conditions.
• Small comparison (general)
  • Water: Green, biocompatible; limited stability at elevated pH/temperature.
  • Methanol/Ethanol: Protic, easy to remove; can participate in acetal/transesterification under acidic/basic conditions.
  • DMSO: Excellent solubilizer; high boiling point complicates removal; hygroscopic.
  • Acetonitrile: Preferred for phosphoramidite chemistry; toxic and flammable.
• Practical tips
  • Filter sterilize aqueous stocks (0.22 µm) for biological testing.
  • Avoid prolonged exposure in basic media to limit nucleobase deamination and glycosidic bond cleavage (literature, general for cytidine analogs).

Storage and Reconstitution

• Item-specific (from Product Data)
  • Storage conditions: Protected from light; Store at -80°C.
  • Shipped in: Dry ice packs + Cold packs.
• General best practices (nucleoside analogs)
  • Upon receipt: Keep frozen. Allow container to equilibrate to room temperature in a desiccator before opening to prevent condensation.
  • Reconstitution solvents: Nuclease-free water or anhydrous DMSO are common; choose based on intended use. For long-term frozen stocks, DMSO can reduce ice crystal stress but is hygroscopic.
  • Concentration: Prepare convenient aliquots (e.g., 10–100 mM) to minimize freeze–thaw cycles.
  • Light protection: Use amber vials or wrap in foil during handling and storage.
  • Stability notes: Aqueous solutions are most stable near neutral pH at ≤4°C for short periods; for longer storage, freeze at −20°C to −80°C. Avoid strongly basic conditions which may promote deamination or glycosidic bond cleavage (literature, general).
• Specifications not provided
  • Exact shelf life, permissible freeze–thaw cycles, and solution stability: Not specified for this item; refer to CoA/Spec Sheet and SDS.

Structure and Identity

Brief: 2'-Deoxy-2'-fluorocytidine (often abbreviated FdC) is a fluorinated deoxycytidine nucleoside analog featuring a single fluorine at the ribose 2'-position.

• Item-specific (from Product Data)
  • SKU: D1500423
  • Product Name: 2'-Deoxy-2'-fluorocytidine
  • Grade: Moligand™
  • CAS: 10212-20-1
  • Storage: Protected from light; Store at -80°C
  • Shipping: Dry ice packs + Cold packs
  • Research use note: For research use only
• Structure (literature/general)
  • Molecular formula: C9H12FN3O4 (literature)
  • Molecular weight: ~245.21 g/mol (literature)
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
  • Core features: A β-D-2-deoxyribofuranose ring bearing a fluorine at the 2' position; N1-glycosidic linkage to the cytosine base (4-amino-2-oxo pyrimidin-1-yl). Hydroxyl groups at 3' and 5' positions typical of deoxynucleosides.
  • 2D description in words: A five-membered furanose (deoxyribose) ring where the 2' substituent is F (instead of H/OH), 3'-OH and 5'-CH2OH remain; the base is a cytosine ring attached via N1 to the anomeric C1' of the sugar (β-configuration).
• Stereochemistry (literature/general)
  • Natural nucleoside configuration at the sugar stereocenters (D-series). 2'-C configuration supports a 2'-F substituent that can bias sugar pucker toward C3'-endo relative to 2'-H, influencing duplex conformation.

Synthetic Utility

• Functional groups and handles (literature/general)
  • Free 3'- and 5'-hydroxyls enable selective protection and downstream elaboration (e.g., phosphitylation). The cytosine base features an exocyclic amine (N4) and a carbonyl (C2) that may require protection (e.g., benzoyl/acetyl) during glycosylation or coupling steps.
  • The 2'-fluoro substituent is non-leaving and conformationally influential, providing a handle to tune nucleic acid geometry without introducing steric bulk.
• Common transformations
  • 5'-O- or 3'-O-phosphoramidite formation using 2-cyanoethyl N,N-diisopropylchlorophosphoramidite (with DIPEA) in dry acetonitrile for solid-phase synthesis.
  • Global or selective silylation (e.g., TBDMS, TBDPS) for temporary protection; cyclic acetals (isopropylidene) are less typical for deoxy sugars but can be employed under controlled conditions.
  • N4-acyl protection (benzoyl/acetyl) prior to sugar chemistry to suppress side reactions.
  • Stepwise phosphorylation (e.g., POCl3 in trimethyl phosphate) to prepare 5'-monophosphate followed by pyrophosphorylation to di-/triphosphate (literature procedures for nucleosides).
• Retrosynthetic value
  • Serves as an advanced intermediate for constructing libraries of 2'-modified deoxycytidine analogs (e.g., base-modified, 5-substituted cytosines) while retaining the 2'-F motif.
• Practical tips
  • Strictly anhydrous conditions and low temperatures benefit phosphoramidite and chlorophosphite steps.
  • Monitor by TLC (silica, MeOH/CH2Cl2 with NH3) or LC–MS; cytidine derivatives often streak—add a base modifier.

Target Specificity

No antibody/biological targeting data are applicable for this small-molecule nucleoside.

• Item-specific: No antigen, epitope, clone, or species reactivity information is provided or relevant for this product.