Uridine 5'-monophosphate , CAS No.U414407

CAS: U414407 Cat. No.: U414407

Synonyms

Uridylic acid | 5'-Uridylic acid | Uridine phosphate | 5'-UMP | Uridine 5'-phosphoric acid

Storage

Room temperature

Visão geral

Information

Uridine 5'-monophosphate (Uridylic acid, 5'-Uridylic acid, Uridine phosphate, 5'-UMP, Uridine 5'-phosphoric acid) is a nucleotide that is used as a monomer in RNA.

Especificações

Sinónimos

Uridylic acid | 5'-Uridylic acid | Uridine phosphate | 5'-UMP | Uridine 5'-phosphoric acid

Condições de armazenamento de armazenamento

Room temperature

Nomes e identificadores

Sorrisos canónicos

OC1C(O)C(OC1CO[P](O)(O)=O)N2C=CC(=O)NC2=O

Application Protocols

Item-specific, validated protocols are not provided for this product; refer to CoA/Spec Sheet if available. Below are literature-style example protocols to guide use.

A. Preparing a nuclease-free UMP stock solution

• Dissolve UMP to 100 mM in nuclease-free water. Adjust pH to 7.5 with NaOH (1 M) if required. Filter-sterilize (0.22 µm) into sterile, RNase-free tubes. Aliquot and store at −20 °C.

B. UMP kinase assay (generation of UDP)

• Buffer: 50 mM Tris–HCl pH 7.6, 10 mM MgCl2, 50 mM KCl.
• Substrates: 1 mM UMP, 2 mM ATP.
• Enzyme: UMP kinase (concentration per supplier’s activity units; e.g., 0.1–1 U/mL).
• Conditions: 30 °C, 30–60 min.
• Quench: Heat at 95 °C for 2 min or add EDTA to 20 mM.
• Analysis: HPLC anion-exchange or HILIC; monitor conversion UMP→UDP.

C. LC–MS calibration standard preparation

• Prepare serial dilutions of UMP in 10 mM ammonium acetate (pH ~7) covering 0.05–50 µM. Store on ice during use; discard after 24 h.

D. Formation of UMP-imidazolide (activation example)

• Dissolve UMP in minimal dry DMF with 2–3 equiv CDI at 0–4 °C under dry N2. Stir 1–2 h while monitoring by analytical ion-exchange HPLC. Quench with water, desalt, and purify by preparative anion-exchange. Keep exposure to moisture minimal to limit hydrolysis.

Note: Optimize conditions for your specific enzyme/system.

Biological Roles

Literature overview of biological function (no clinical claims)

• Central metabolite: UMP is the entry pyrimidine nucleotide formed from orotidine 5'-monophosphate (OMP) by OMP decarboxylase in de novo pyrimidine biosynthesis. It is subsequently phosphorylated to UDP and UTP, and aminated to CTP via UDP/UTP intermediates.
• RNA precursor: The uracil base in UMP is one of the four canonical ribonucleotides constituting RNA (as phosphodiester-linked residues in polynucleotide chains).
• Sugar activation pathways: UTP derived from UMP forms UDP-sugars (e.g., UDP-glucose), key donors in glycoconjugate and glycogen biosynthesis; UMP is thus a precursor node in glycosyltransfer reactions.
• Salvage pathways: UMP participates in nucleotide salvage via uridine–uridine kinase cycles; uridine can be phosphorylated to UMP by uridine–cytidine kinases.
• Signaling/energetics: While UMP itself is not a primary high-energy currency, interconversion with UTP and UDP intersects with cellular signaling and enzymatic regulation.
• Analytical biomarker: Measured in metabolomics to assess pyrimidine pathway flux, nucleotide pools, and responses to metabolic perturbations.

Biochemical properties relevant to function

• Ionization: At physiological pH, UMP predominantly bears a dianionic phosphate, favoring interactions with Mg2+/divalent cations and protein active sites.
• Hydrogen bonding: Uracil functional groups support specific base-pairing and recognition by enzymes and RNA-binding proteins.

Buffer Applications

Applicability

• UMP is not a conventional buffer component and is not typically used to set or maintain pH.

Practical notes for solutions

• Preparation: Dissolve UMP in nuclease-free water; adjust pH with NaOH or HCl only as needed after dissolution. Typical working concentrations range from micromolar (analytical standards) to millimolar (enzyme assays).
• Compatible buffers: Tris, HEPES, MOPS, and phosphate buffers in the pH 6.5–8.5 range are commonly used in assays that include UMP.
• Ionic considerations: UMP contributes phosphate and counterions to the medium; account for this when designing phosphate-sensitive experiments or when Mg2+ chelation effects are relevant.

If a buffering capacity is required, select an appropriate buffer system based on the target pH and enzyme compatibility, and treat UMP solely as a substrate/standard within that buffered system.

Green Alternatives

Context

• As a biogenic, highly polar nucleotide used mainly in aqueous media, UMP aligns well with green chemistry principles regarding solvent choice (water as the primary solvent). Green alternatives are thus more about process conditions and buffer systems than replacing the molecule itself.

Greener practice considerations

• Solvent: Prefer water or aqueous, pH-controlled, volatile buffers (e.g., ammonium acetate/formate) for analytical workflows to minimize phosphate waste.
• Energy: Conduct enzymatic reactions at ambient temperature where possible; avoid unnecessary heating that accelerates hydrolysis.
• Waste minimization: Scale reactions/assays appropriately; use microplate formats to reduce reagent consumption. For HPLC/LC–MS, use short columns and lower flow rates to reduce solvent waste.
• Buffer substitution: Where phosphate buffer is not mechanistically required, use HEPES, MOPS, or Good’s buffers to limit inorganic phosphate discharge.

Comparison (literature-based)

• Traditional approach: High-ionic-strength phosphate buffers; large-volume batch assays; non-volatile salts for LC.
• Greener approach: Volatile buffers for MS compatibility; microfluidic/microplate assays; on-demand preparation of small-volume stocks; recyclable plasticware where validated.

Trade-offs

• Volatile buffers can alter enzyme activity profiles compared with phosphate. Optimization may be required to maintain activity while improving environmental footprint.

Pharmaceutical Uses

Scope and limitations

• This product is for research use only (per Product Data). No medical or clinical claims are made.

Formulation/manufacturing context (literature/general)

• Excipient/medium component: Uridine nucleotides and nucleosides are sometimes incorporated into cell culture media or bioprocess supplements for biomanufacturing process development. UMP itself may serve as a defined nutrient or metabolic standard in process analytics.
• Reference standard: Used as a chemical reference in QC/analytical method development for nucleotides (e.g., HPLC/LC–MS system suitability, retention time markers, calibration curves).
• Lyophilized formulations: UMP can be prepared as lyophilized standards for stability and ease of reconstitution in analytical labs.

Regulatory/compendial status

• No pharmacopeial monograph details are provided for this item; refer to CoA/Spec Sheet and applicable pharmacopeias if compendial compliance is required for your workflow.

Practical considerations

• Ensure the grade/purity and bioburden/nuclease specifications match intended use. For GMP-adjacent method development, request extended QC data and lot traceability.

Physical Properties

Item-specific facts (from Product Data)

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

Literature/general properties (for uridine 5'-monophosphate, free acid)

• Physical state: Typically a white to off-white crystalline solid; hygroscopic tendencies are common among nucleotide salts/acids.
• Solubility: Highly soluble in water; poor solubility in most anhydrous organic solvents (alcohols only slightly to moderately, depending on ionization state).
• pKa (approximate, literature):
  • Phosphate pKa1 ~1.0–1.2 (first deprotonation)
  • Phosphate pKa2 ~6.0–6.5 (second deprotonation)
  • Uracil N3 (ring NH) pKa ~9–9.5 (very weakly basic/acidic center depending on context)
• Partitioning: Strongly hydrophilic; negligible logP in neutral form; logD is strongly negative at physiological pH due to dianionic phosphate.
• Optical rotation: Not commonly reported for the free acid; nucleotides are chiral due to ribose.
• Melting point: Often reported as “decomposes on heating” rather than a sharp melting point (typical for nucleotides).
• UV absorption (literature): Strong band from uracil base, λmax ~260–262 nm in water (ε on the order of 10^4 L·mol−1·cm−1), pH-dependent fine structure.
• Hygroscopicity: Nucleotides can absorb moisture; drying over P2O5 or in vacuo at ambient temperature is common before analytical weighing.

Notes

• Exact numeric specifications (water content, ash, metal content, UV cutoff, density, refractive index) are not specified for this item; refer to CoA/Spec Sheet.

Quality and Grades

Item-specific quality details

• Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
• Stabilizers/Counterions: Not specified for this item; refer to CoA/Spec Sheet. UMP may be offered as the free acid or as a salt (e.g., disodium); verify on the label/CoA as properties and solubility can differ.

General guidance on grades for nucleotides

• Research grade: Suitable for general biochemical assays, molecular biology workflows, enzymatic reactions, and small-molecule libraries. May have broader impurity limits than analytical reference standards.
• Molecular biology grade: Typically tested for DNase/RNase/protease contamination; critical for enzymatic polymerization, kinase assays, and RNA-related workflows.
• HPLC grade (reference/API standard context): Emphasizes chromatographic purity with low UV-absorbing impurities; often accompanied by chromatograms and impurity profiling.

What to verify on the CoA/Spec Sheet

• Identity confirmation: HPLC purity, NMR, MS; UV λmax and extinction coefficient may be provided for QC.
• Inorganic profile: Residual salts (Na+, K+, phosphate), sulfate/ash content, and water content (Karl Fischer) if applicable.
• Microbial/enzymatic contaminants: RNase/DNase/protease activities, endotoxin (if relevant to your application).
• Residual solvents: Not typically an issue for aqueous-processed nucleotides, but check limits when relevant.

Implications for use

• For sensitive enzymatic assays, prioritize nuclease-tested lots. For quantitative analytical work, request a CoA with full chromatographic data and water content.

Reaction and Applications

Scope

• UMP is primarily used in biochemical and enzymatic contexts rather than classical organic reactions. It serves as a substrate, standard, or intermediate in nucleotide metabolism and RNA-related processes.

Representative applications (literature)

• Enzymatic phosphorylation: Substrate for nucleotide monophosphate kinases (e.g., UMP kinase) to generate UDP using ATP as phosphate donor.
• Nucleic acid metabolism studies: Baseline metabolite in the de novo pyrimidine pathway (formed from OMP by OMP decarboxylase); used as a standard in metabolomics (LC–MS, HILIC) and enzyme kinetics.
• Polymerase/ligase assays: Component or control in RNA polymerase reactions and ligase reactions when generating or extending uridine-containing RNAs (though UTP is the direct polymerase substrate).
• Chemical biology: Competitive inhibitor/ligand in binding studies of nucleotide-binding enzymes; component for riboswitch and aptamer selection assays when presented as part of libraries.
• Analytical reference: Calibration standards for HPLC/LC–MS quantitation of nucleotides in biological matrices.

Practical tips

• Use nuclease-free solutions and plasticware; include 1–5 mM Mg2+ when working with kinases/transferases if required by the enzyme.
• Maintain pH 7.2–8.0 for enzyme assays; store working solutions on ice, and avoid repeated freeze–thaw.
• For LC–MS, prepare in volatile buffers (ammonium acetate/formate); avoid high phosphate in mobile phase as it suppresses ionization.

Reaction Conditions

General guidance (literature; adapt to your specific enzyme/system)

• Enzymatic phosphorylation to UDP: UMP (0.1–10 mM), ATP (slight excess), MgCl2 (5–10 mM), Tris–HCl or HEPES buffer pH 7.5–8.0, 25–37 °C; time 0.5–2 h depending on enzyme loading. Monitor by HPLC or TLC (PEI-cellulose, LiCl mobile phases).
• Further phosphorylation to UTP: UDP kinase systems or acetate kinase/pyruvate kinase coupled systems; similar pH/temperature; regenerated ATP systems (PEP/PK) maintain high conversions.
• Chemical activation to phosphorimidazolide: UMP with CDI (1,1′-carbonyldiimidazole) or EDC/imidazole in anhydrous DMF/DMSO with minimal water; keep temperature 0–25 °C; work rapidly to minimize hydrolysis; quench and purify by ion-exchange.
• RNA ligation/templated assembly: Use activated UMP derivatives (e.g., UMP-imidazolide) in buffered aqueous media (pH 7.5–8.5), Mg2+ (10–50 mM) or Zn2+ as catalysts; monitor conversion by PAGE or HPLC.

Stability considerations

• Hydrolysis: Accelerated under strong acid/base and at elevated temperatures; avoid prolonged exposure above 40 °C. Maintain neutral to slightly basic pH for most enzyme reactions.
• Metal ion effects: Mg2+ typically beneficial; high concentrations of transition metals can promote degradation/oxidation and should be sequestered (e.g., with EDTA) in non-enzymatic workflows.

Analytics

• LC–MS: Prefer volatile buffers (≤20–50 mM ammonium acetate/formate); negative ESI often yields stronger signals for phosphate-containing analytes. HILIC or anion-exchange chromatography separates UMP/UDP/UTP efficiently.

Safety and Handling

Item-specific hazard information

• Signal word: Not specified for this item; refer to SDS.
• H-statements: Not specified for this item; refer to SDS.
• GHS classification/pictograms: Not specified for this item; refer to SDS.

General safety guidance (literature/practice for nucleotides)

• Expected hazard profile: UMP is generally considered low hazard for laboratory handling; however, always consult the SDS for authoritative information.
• PPE: Laboratory coat, safety glasses, and appropriate disposable gloves (e.g., nitrile). Use dust mask/respirator if dusts/aerosols may be generated during weighing.
• Handling: Avoid generating dust. Work on a clean, dry surface. For solution prep, use clean, nuclease‑free water to avoid enzymatic degradation in downstream applications.
• Incompatibilities: Strong oxidizers and strong acids/bases may lead to degradation; phosphate ester hydrolysis is accelerated under strongly acidic or basic conditions and at elevated temperature. Avoid nucleases if biological activity assays are intended.
• First aid (general):
  • Inhalation: Move to fresh air; seek medical advice if symptoms occur.
  • Skin/eye contact: Rinse with water for several minutes; remove contaminated clothing; seek medical advice if irritation persists.
  • Ingestion: Rinse mouth; do not induce vomiting; seek medical attention if unwell.
• Spill/leak: Avoid dust formation; sweep or vacuum using HEPA-equipped device; place in appropriate container for disposal.
• Waste disposal: Dispose in accordance with local regulations; aqueous solutions are typically disposed as non-hazardous chemical waste unless contaminated.

Note: Always defer to the product’s SDS and institutional EHS policies.

Solvent Selection

Applicability

• UMP is a highly polar, ionic nucleotide; solvent choice primarily concerns preparing aqueous buffers/solutions rather than organic reaction media.

General solvent behavior (literature)

• Water: Freely soluble; dissolution is favored near neutral to slightly basic pH where the phosphate is deprotonated. Nuclease‑free water recommended for biology workflows.
• Alcohols: Limited solubility in lower alcohols; solubility improves with added water.
• Polar aprotic solvents: Essentially insoluble in anhydrous DMF/DMSO without water; however, small volumes of DMSO can be used to prepare concentrated stock solutions before diluting into buffer if necessary.
• Nonpolar solvents: Insoluble.

Buffer compatibility

• Common buffers: Tris, HEPES, MOPS, phosphate buffer (consider total phosphate load when UMP is present), pH 6.5–8.5 typical for stability and enzyme assays.
• Ionic strength: 50–200 mM NaCl often used for enzyme assays; Mg2+ (1–10 mM) frequently required for kinases/transferases utilizing UMP/UDP/UTP.

When to choose UMP vs alternatives

• UMP is selected when a monophosphate nucleotide donor/acceptor or metabolite standard is needed (e.g., kinase substrate/standard). Use UDP/UTP when higher phosphoryl transfer potential or glycosyl activation (UDP-sugars) is required.

Practical notes

• Adjust pH after dissolution; UMP solutions are mildly acidic. Filter-sterilize (0.22 µm) for biological work; avoid autoclaving to prevent degradation.

Storage and Reconstitution

Item-specific storage

• Storage conditions provided: Room temperature.
• Shipped in: Not specified for this item; refer to CoA/Spec Sheet.

General guidance (literature/practice for nucleotides)

• Solid form: Store tightly capped in a dry place, protected from moisture and light. For long-term retention of analytical properties, many labs store at 2–8 °C or desiccated at room temperature. Avoid high humidity; consider a desiccator.
• Reconstitution: Dissolve in nuclease-free water or appropriate buffer. Adjust pH to 7.0–7.5 after dissolution if needed. Filter-sterilize for biological applications.
• Working solutions: Aliquot to avoid repeated freeze–thaw. Store at −20 °C for weeks to months or at 4 °C for short-term (days). Avoid autoclaving; if sterilization is required, use filtration.
• Stability notes: UMP solutions are generally stable near neutral pH at 4 °C for several days; hydrolysis accelerates at elevated temperature and at pH <3 or >9.

Label guidance

• Clearly label concentration, pH, buffer composition, preparation date, and lot number. Track freeze–thaw cycles.

Disclaimer

• Where storage guidance in the Product Data differs from general practice, prioritize the Product Data and the product label. For definitive stability limits and specifications, consult the CoA/Spec Sheet and SDS.

Research use only

• Per Product Data: For research use only.

Structure and Identity

Item-specific facts (from Product Data)

• Product name: Uridine 5'-monophosphate (UMP)
• SKU: U414407
• Storage conditions: Room temperature (per listing)
• CAS: Not specified for this item; refer to CoA/Spec Sheet.
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.

Literature/general identity information

• Common synonyms: UMP; uridylic acid; uridine monophosphate (5'-UMP)
• Molecular formula (literature, free acid): C9H13N2O9P
• Molecular weight (literature, free acid): ~324.18 g/mol
• Structural features (descriptive):
  • Nucleoside monophosphate comprising the pyrimidine base uracil (2,4-dioxopyrimidine) N1-glycosidically linked to a D-ribofuranose sugar.
  • A phosphate monoester at the 5'-hydroxyl of ribose (primary phosphate; tetrahedral P(V)).
  • Heteroaromatic ring (pyrimidine) with two carbonyls (C2=O, C4=O), an endocyclic imide-like NH at N3.
  • Multiple hydrogen-bond donors/acceptors; highly polar, zwitterion/ionic forms depending on pH.
• Stereochemistry: Ribose is D-configuration with β-anomeric linkage to uracil; typical ribofuranose ring adopts an envelope conformation.

2D description in words

• A six-membered uracil ring (pyrimidine-2,4-dione) attached via N1 to C1' of a five-membered ribofuranose. The ribose bears hydroxyls at 2' and 3', and a phosphate group esterified to the 5' carbon (–CH2–O–P(O)(OH)2). The molecule presents multiple polar functional groups (two carbonyls, three hydroxyls, phosphate diacid), driving strong aqueous solvation.

Synthetic Utility

Role in synthesis (literature)

• Biocatalytic transformations: UMP is a substrate for UMP kinases producing UDP, which in turn feeds glycosyltransfer reactions via UDP-sugars. This underpins enzymatic synthesis of glycoconjugates and oligosaccharides.
• Nucleic acid construction: While polymerases employ nucleotide triphosphates directly (UTP), UMP can be enzymatically phosphorylated to UTP in situ, serving as a precursor in chemoenzymatic RNA synthesis workflows.
• Labeling/derivatization: The phosphate and ribose hydroxyls enable selective chemical modification (e.g., formation of phosphate esters or conversion to phosphoramidates) for probe design, immobilization, or activation to phosphorimidazolides for template-directed ligation chemistry.
• Reference/standard: Used as a benchmark compound for developing HILIC/ion-pair reversed phase LC methods targeting nucleotide mixtures.

Reactivity highlights

• Phosphate chemistry: Formation of anhydrides, mixed esters, and activation under carbodiimide or imidazole-based protocols. Careful pH control and Mg2+ presence modulate reactivity and aggregation.
• Base moiety (uracil): Participates in hydrogen bonding; mild N3 deprotonation under basic conditions can affect tautomeric equilibria but is generally non-reactive in standard synthetic routes.

Practical considerations

• Protecting-group strategy (chemical synthesis): 2',3'-di-O-protection on ribose and temporary masking/activation of the phosphate are typical if conducting multi-step modifications.

Target Specificity

Not applicable to this product type.

• UMP is a small-molecule nucleotide, not an antibody, probe, or targeted biologic. It does not have clone, isotype, or species specificity attributes.
• For enzyme assays, consult literature for enzyme selectivity toward UMP versus other nucleotides, but no item-specific target specificity is provided.

Perguntas frequentes

How should this product be stored?

Store at room temperature.

What are the CAS number, molecular formula and molecular weight?

The CAS Number is U414407.

What documentation is provided?

Available product documentation, including Certificates of Analysis (COA), Safety Data Sheets (SDS), and specification sheets, is shown in the product document area. Document availability and access follow the current site policy.