Thymine riboside, L- - ≥97% , CAS No.642082-80-2

CAS: 642082-80-2 Cat. No.: T960741 PubChem CID: 1715220

GRADE & PURITY ≥97%

Storage

Room temperature

Specifications

Specifiche e purezza

≥97%

Condizioni di conservazione di stoccaggio

Room temperature

Purezza

≥97%

Nomi e identificatori

• Sorrisi canonici: CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)O
• IUPAC Name: 1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
• InChIKey: DWRXFEITVBNRMK-AZRUVXNYSA-N
• INCHI: 1S/C10H14N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m0/s1
• Isomeri SMILES: CC1=CN(C(=O)NC1=O)[C@@H]2[C@H]([C@H]([C@@H](O2)CO)O)O
• CAS alternativo: 26879-47-0
• PubChem CID: 1715220

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Nucleosides, nucleotides, and analogues
    • Classe Pyrimidine nucleosides

• Kingdom: Organic compounds
• Superclass: Nucleosides, nucleotides, and analogues
• Classe: Pyrimidine nucleosides
• Subclass: Not available
• Intermediate Tree Nodes: Not available
• Direct Parent: Pyrimidine nucleosides
• Alternative Parents: Glycosylamines Pentoses Pyrimidones Hydropyrimidines Tetrahydrofurans Heteroaromatic compounds Vinylogous amides Ureas Lactams Secondary alcohols Oxacyclic compounds Azacyclic compounds Primary alcohols Organopnictogen compounds Organonitrogen compounds Organic oxides Hydrocarbon derivatives
• Molecular Framework: Aromatic heteromonocyclic compounds
• Substituents: Pyrimidine nucleoside - Glycosyl compound - N-glycosyl compound - Pentose monosaccharide - Pyrimidone - Hydropyrimidine - Monosaccharide - Pyrimidine - Vinylogous amide - Tetrahydrofuran - Heteroaromatic compound - Urea - Secondary alcohol - Lactam - Organoheterocyclic compound - Oxacycle - Azacycle - Hydrocarbon derivative - Organopnictogen compound - Organooxygen compound - Organonitrogen compound - Primary alcohol - Alcohol - Organic oxygen compound - Organic oxide - Organic nitrogen compound - Aromatic heteromonocyclic compound
• Descrizione: 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

Data sources

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.

DOI: 10.1186/s13321-016-0174-y

Proprietà chimiche e fisiche

• Peso molecolare: 258.230 g/mol
• XLogP3: -1.600
• Hydrogen Bond Donor Count: 4
• Hydrogen Bond Acceptor Count: 6
• Rotatable Bond Count: 2
• Exact Mass: 258.085 Da
• Monoisotopic Mass: 258.085 Da
• Topological Polar Surface Area: 119.000 Ų
• Heavy Atom Count: 18
• Formal Charge: 0
• Complexity: 409.000
• 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

Application Protocols

No item‑specific, validated application protocols are provided for this product. As general guidance for laboratory use:

• Preparation of stock solutions: Dissolve in water or DMSO to a convenient concentration (e.g., 10–100 mM for analytical stocks). Filter sterilize (0.22 µm) if using in cell‑free biochemical assays. Record exact solvent and concentration for reproducibility.
• HPLC analysis (general): Use reverse‑phase C18 with aqueous buffer (e.g., 10–50 mM phosphate, pH 6–7) and MeOH or ACN modifier. Monitor at ~260–270 nm. Validate resolution if assessing enantiopurity with a chiral stationary phase.
• Solid‑phase synthesis precursor preparation: If converting to a phosphoramidite, follow nucleoside protection and coupling protocols under anhydrous conditions; verify by 31P NMR and LC‑MS.

For application‑specific, item‑level instructions (including recommended dilutions or controls), consult the CoA/Spec Sheet or contact Technical Support. All uses are for research only.

Biological Roles

Item-specific biological data are not provided for this product. The following is general, literature-based context.

• Natural counterpart: The D‑enantiomer of thymine riboside (D‑5‑methyluridine, ribothymidine; m5U, rT) occurs widely in biology, notably at position 54 in many tRNAs, contributing to tRNA structure and thermostability via base stacking and tertiary interactions.
• L‑enantiomer context: L‑thymine riboside is not naturally occurring in standard biochemistry. Due to its mirror‑image sugar configuration, it is generally not a substrate for native nucleoside transporters or metabolizing enzymes (kinases, phosphorylases) that exhibit strict D‑specificity. This property is leveraged to study stereospecific recognition by enzymes and transport systems in vitro.
• Nuclease resistance (literature): Oligonucleotides assembled from L‑ribonucleosides are typically resistant to degradation by canonical nucleases, enabling use as stable ligands in biochemical binding studies (e.g., mirror‑image aptamers, “Spiegelmers”).
• Binding/recognition: While base pairing rules (A–U/T complementarity) are preserved within the mirror‑image framework, L‑oligonucleotides do not form canonical duplexes with natural D‑RNA/DNA; instead, they can form homochiral duplexes with L‑strands (literature observations).
• Analytical standards: The L‑nucleoside can serve as a negative control or internal standard in assays designed to quantify D‑nucleosides or to confirm chiral selectivity of enzymes.

All statements above are general literature insights and not item‑specific performance claims.

Buffer Applications

This product is a ribonucleoside and is not a buffer component. It does not constitute a defined buffering system and is not typically used to control pH.

Practical guidance:

• For dissolving and assaying L‑thymine riboside, use standard biological buffers appropriate to your system (e.g., phosphate‑buffered saline [PBS], HEPES, Tris) in the pH range 6.5–8.0, where the nucleoside remains neutral and stable.
• Avoid strongly acidic or basic buffers for prolonged incubations, which can promote N‑glycosidic cleavage or sugar/base degradation.
• When UV‑quantifying near 260–270 nm, choose buffers with low UV absorbance in that region (e.g., phosphate, HEPES) and verify baseline.

If you require a specific buffering recipe or ionic strength for your assay, consult application notes for your assay type. The nucleoside itself provides no intrinsic buffering capacity in the physiological pH range.

Green Alternatives

As a solid nucleoside, the greenness considerations center on solvent and reagent choices during handling, purification, and derivatization rather than on the compound itself.

Greener choices (general literature guidance):

• Solvents for dissolution and workup:
  • Prefer water and ethanol where feasible for preparation of assay stocks and recrystallizations.
  • Substitute 2‑propanol for acetone in some crystallizations/extractions when compatible.
  • Limit use of high‑boiling polar aprotics (DMF/DMSO) to steps where strictly necessary; recover/recycle when possible.
• Protection and coupling chemistry:
  • Consider green acetonide formation using catalytic acids in greener solvents (ethanol/water) versus chlorinated solvents, when substrate stability permits.
  • For phosphoramidite chemistry, explore less hazardous activators (e.g., ethylthiotetrazole) and minimize excess reagents.
• Purification:
  • Favor aqueous normal‑phase or reverse‑phase chromatography with alcohol modifiers over chlorinated eluents; utilize gradient methods to reduce solvent consumption.
• Energy and waste:
  • Employ microscale test reactions to reduce waste, and recover solvents via distillation where purity allows.

Illustrative comparison (general):

• Water/ethanol vs. DMF/DMSO: lower toxicity and easier removal; may limit maximum solubility or compatibility with moisture‑sensitive steps.
• Ethyl acetate vs. dichloromethane for extractions: safer profile, albeit with higher polarity and potential emulsions.

Note: Selection must balance green metrics with substrate stability (avoid strong acid/base that can cleave the N‑glycosidic bond).

Pharmaceutical Uses

No item-specific pharmacopeial status, grade, or excipient role is provided for this product.

General, non-clinical context for nucleosides (literature-based):

• Role in development workflows: Non-natural nucleosides, including L‑configured analogs, are used in discovery chemistry as reference standards, enzyme selectivity probes, and building blocks for modified oligonucleotides evaluated in preclinical research settings. Such uses focus on physicochemical characterization, target engagement studies, and stability assessments — not on clinical administration.
• Excipient/formulation relevance: Nucleosides are not commonly employed as formulation excipients. However, they may be included in in vitro test systems or as analytical standards in quality control methods for nucleoside‑containing products.
• Regulatory considerations: If intended for GMP‑related analytical purposes, users typically require documented identity/purity, validated analytical methods, and traceability (CoA, lot records). Enantiomeric purity is particularly important for L‑/D‑pairs.

This product is supplied strictly for research use only, as stated in the Product Data. No medical, diagnostic, or therapeutic use is implied.

Physical Properties

Item-specific physicochemical specifications (BP/MP, density, UV cutoff, metal limits, residual solvents, etc.): Not specified for this item; refer to CoA/Spec Sheet.

General/literature information for L‑thymine riboside (L‑5‑methyluridine) — for context only, not product specifications:

• Phase/appearance: typically a white to off‑white crystalline solid for nucleosides.
• Solubility profile: high aqueous polarity; readily soluble in water; soluble in polar protic/apyrotic solvents (e.g., methanol, ethanol, DMSO), sparingly soluble in less polar solvents. Solubility increases with temperature and ionic strength.
• Acid/base behavior: weakly basic ring nitrogens and weakly acidic ring NH; overall neutral at physiological pH; multiple hydrogen-bond donors/acceptors; pKa values for nucleoside tautomerizations fall outside standard buffering ranges (literature, qualitative).
• UV absorbance: pyrimidine nucleosides exhibit a π→π* absorbance band in the near‑UV; thymine/ribothymidine typically show λmax in the mid‑260–270 nm range (literature), useful for HPLC/UV quantification.
• Hygroscopicity: nucleosides may absorb moisture; drying under vacuum at ambient/mild temperatures is commonly employed prior to moisture-sensitive derivatizations (general practice).
• Thermal behavior: many nucleosides darken/decompose on melting rather than showing a sharp MP; DSC/TGA recommended if a precise transition is required (general guidance).

Note: For any numerical property required for your process validation (e.g., water content, specific rotation, extinction coefficient), consult the product’s CoA/Spec Sheet or request characterization data.

Quality and Grades

• Item-specific grade/purity: Not specified for this item; refer to CoA/Spec Sheet.

General guidance on quality considerations for nucleosides:

• Research grade vs. higher‑purity grades: For biochemical assays, oligonucleotide synthesis, and chiral enzymology, impurities such as closely related nucleoside analogs, inorganic salts, or residual solvents can impact results. Typical QC includes HPLC purity, NMR identity, MS, and water content (Karl Fischer). Where chirality is critical (L vs D), an orthogonal assessment such as optical rotation and/or chiral HPLC is recommended.
• UV transparency: For HPLC/UV monitoring at ~260–270 nm, low baseline drift and absence of UV‑active impurities are desirable; some suppliers offer “HPLC” or “BioUltra” grades with stringent UV specs. If your application is quantitative by UV, request the extinction coefficient or verify via calibration.
• Residual moisture: Free 2′/3′‑OH nucleosides can be moderately hygroscopic; high water content may hinder downstream derivatizations (e.g., phosphitylation). Drying specifications and packaging under desiccation mitigate this.
• Enantiomeric purity: This product is the L‑enantiomer; for biochemical studies of stereospecificity or for mirror‑image oligonucleotide assembly, confirm enantiomeric excess (ee) on the CoA or by independent testing.
• Stabilizers/additives: Not applicable/typically none for solid nucleosides; if present, they must be declared on the CoA.

Recommendation: Align the selected grade with your intended use (analytical reference vs. synthesis precursor) and request a current CoA for definitive, item‑specific specifications.

Reaction and Applications

This L‑nucleoside serves as a useful probe and precursor in nucleic acids chemistry and enzymology.

• Applications in research (general):
  • Stereochemical probes: L‑ribosides are mirror‑image counterparts to natural D‑nucleosides and are widely used to interrogate enzyme stereospecificity in nucleoside phosphorylases, kinases, and glycosidases.
  • Oligonucleotide chemistry: After suitable protection (e.g., 5′‑O‑DMT, 2′/3′‑O‑silyl or acetal protections) and conversion to 3′‑ or 5′‑phosphoramidites, L‑ribonucleosides enable assembly of L‑RNA strands. Such oligos exhibit high resistance to natural nucleases and are valuable for binding/recognition studies (Spiegelmer concept, literature).
  • Reference standards: Employed as analytical comparators in HPLC or LC‑MS to resolve L/D isomers or to validate chiral analytical methods.
• Transformations (typical):
  • Selective protection of the 5′‑hydroxyl (DMT, MMTr) and temporary protection of 2′/3′‑diols (acetonide, TIPDS, TBDMS) under mild, anhydrous conditions.
  • Glycosyl chemistry: While the glycosidic bond is pre‑formed, the nucleobase can be further modified at N3 (alkylation protection) or at the 5‑methyl group (radical halogenation followed by substitution, literature) to access analogs.
  • Phosphate installation: Phosphorylation (POCl3/pyridine or phosphoramidite routes) to generate monophosphates or activated amidites for solid‑phase synthesis.
• Practical notes:
  • Thorough drying of the nucleoside and glassware is crucial to high yields in acylation/silylation/phosphitylation.
  • Maintain moderate temperatures and avoid strong base for prolonged times to limit anomerization or N‑glycosidic cleavage.

All reaction guidance above reflects general literature practices for ribonucleosides; optimize conditions empirically for the L series.

Reaction Conditions

The following conditions reflect general literature practices for ribonucleoside manipulation and are provided as non‑product‑specific guidance. Optimize for the L‑series as needed.

• 5′‑O‑DMT protection:
  • Typical: DMT‑Cl (1.2–2.0 eq), pyridine or CH2Cl2/DMAP, 0–25 °C, 1–4 h. Quench with MeOH. Workup by aqueous bicarbonate and extract. Monitor by TLC/HPLC (UV ~260–270 nm).
• 2′/3′‑Diol protection:
  • Acetonide: 2,2‑dimethoxypropane (3–10 eq), catalytic acid (e.g., CSA/p‑TsOH), acetone or acetone/MeCN, 0–25 °C, 1–12 h; or Dean–Stark in toluene for water removal.
  • Silyl: TBDMS‑Cl (2–4 eq) with imidazole in DMF (rt to 50 °C, 2–16 h); TIPDS‑Cl2 (1.1–1.5 eq) with imidazole in DMF or pyridine.
• Phosphitylation (amidite formation):
  • 2‑cyanoethyl N,N‑diisopropylchlorophosphoramidite (1.5–2.0 eq), DIPEA (2–4 eq), anhydrous CH2Cl2/THF, 0–25 °C, 0.5–2 h under inert gas. Exclude moisture strictly.
• Monophosphate synthesis:
  • POCl3 (1.1–1.5 eq) in trimethyl phosphate or pyridine at 0–5 °C, then neutralize and purify by reverse‑phase chromatography.
• C5‑functionalization (on the thymine ring):
  • Radical bromination (NBS/AIBN) in CCl4 or greener alternatives (PhCF3, ACN) at reflux; follow with substitution or cross‑coupling (literature; ensure conditions compatible with glycosidic stability).

Typical yields depend strongly on protection patterns and substrate purity; consult primary literature or internal method development for expected ranges. Always assess integrity by NMR and HPLC, verifying retention of the L configuration (e.g., by chiral HPLC or optical rotation).

Safety and Handling

Item-specific hazard classification and statements:

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

General laboratory safety guidance (not a substitute for the SDS):

• Expected hazards: Nucleosides like thymine ribosides are generally of low acute toxicity; nonetheless, handle as a laboratory chemical. Avoid inhalation of dusts and contact with eyes/skin. No special reactivity hazards are typical for this class.
• Personal protective equipment: lab coat, appropriate gloves (e.g., nitrile), and splash‑resistant safety glasses. Use a dust mask or operate in a fume hood if powder handling could generate airborne particulates.
• Handling: minimize moisture uptake; keep containers tightly closed. Use clean, dry tools to prevent cross‑contamination. For preparative work, weigh quickly in a low‑humidity environment.
• Incompatibilities: strong oxidizers may degrade the nucleobase; strong acids/bases can hydrolyze the N‑glycosidic bond or cause sugar/base degradation, especially at elevated temperatures.
• First aid (overview): if on skin/eyes, rinse with water for several minutes; if inhaled, move to fresh air; if ingested, rinse mouth with water. Seek medical attention if symptoms persist. Provide the SDS to responders.
• Spills & disposal: collect solid spills with minimal dust generation; place in appropriate container for chemical waste. Dispose of according to institutional and local regulations.
• Fire: use water spray, CO2, dry chemical, or foam. Combustion may produce COx/NOx; firefighters should wear self‑contained breathing apparatus.

Always consult the product‑specific SDS prior to use.

Solvent Selection

Thymine riboside, L- is a highly polar, hydrogen‑bond‑rich ribonucleoside. Solvent choice should reflect its polarity, intended operation (dissolution vs. derivatization), and sensitivity of the N‑glycosidic bond.

• Polarity/miscibility (general):
  • Readily soluble in water; excellent solubility in DMSO; good solubility in methanol/ethanol; limited solubility in acetonitrile; poor in nonpolar solvents (Et2O, hexanes, toluene).
  • For analytical HPLC, aqueous buffers with MeOH or ACN modifiers are standard; detection near 260–270 nm.
• Typical use scenarios:
  • Biochemical assays: dissolve in water or buffered aqueous media (pH ~6–8). Filter sterilize (0.22 µm) if sterility is required.
  • Derivatization/synthesis: employ anhydrous polar aprotic solvents (e.g., DMF, DMSO, or pyridine) after azeotropic drying (with MeOH or toluene) to minimize water during protection/phosphitylation.
• Practical tips:
  • If preparing concentrated stock solutions, DMSO affords high solubility and stability; subsequently dilute into aqueous media.
  • Avoid strong basic media in protic solvents for extended periods to reduce risk of glycosidic cleavage or base epimerization.
• Comparison (general guidance):
  • Water: green, biocompatible; best for bioassays; limited for moisture‑sensitive steps.
  • Methanol/Ethanol: good balance of solubility/volatility; suitable for preparative work and crystallizations.
  • DMSO/DMF: excellent solvents for high concentrations and coupling chemistry; require careful removal and attention to residuals.

Note: For chromatography, select buffers that do not absorb strongly near 260–270 nm if UV quantification is required.

Storage and Reconstitution

• Storage conditions (item-specific): Room temperature (per Product Data). Keep container tightly closed.
• Shipping: Not specified for this item; refer to CoA/Spec Sheet.

General handling guidance for nucleosides:

• Protect from excessive humidity; store in a dry place. For long‑term storage, consider keeping the original sealed container inside a desiccator.
• If frequent access is expected, aliquot into smaller vials to minimize moisture uptake and headspace exposure.
• Drying prior to moisture‑sensitive reactions: desiccate under high vacuum at ambient to mild temperature to remove adsorbed water.

Reconstitution (general suggestions):

• Aqueous use: Dissolve in high‑purity water or appropriate buffer (pH 6.5–8.0). Gentle warming (≤40 °C) and vortexing/sonication can aid dissolution. Filter through 0.22 µm for sterile applications.
• Organic stocks: For high‑concentration solutions, DMSO or methanol are effective; record solvent and concentration. Store solutions refrigerated if compatible, and use amber vials to limit UV exposure when quantifying by UV.
• Freeze–thaw: Solid material tolerates ambient storage; for solutions, minimize freeze–thaw cycles by aliquoting. Inspect for precipitation or discoloration before use.

Always defer to the SDS and CoA for any item‑specific instructions beyond the general guidance above. Research use only.

Structure and Identity

Thymine riboside, L- is the L-enantiomer of ribothymidine (5‑methyluridine), a pyrimidine ribonucleoside comprised of thymine (5‑methyluracil) N1‑glycosidically linked to L‑ribofuranose.

• Item-specific identifiers from Product Data:
  • CAS: 642082-80-2
  • InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
  • SMILES: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
  • Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• Structural features (general/literature description):
  • Core base: thymine (5‑methyluracil), a 2,4‑dioxo pyrimidine bearing a 5‑methyl substituent.
  • Sugar: L‑ribofuranose (four chiral centers in L configuration) with free 2′‑ and 3′‑hydroxyls; typical nucleosides adopt a β‑N1 glycosidic linkage to the base.
  • Stereochemistry: global sugar configuration is L (mirror image of the natural D‑ribose series). No additional stereocenters in the aglycone.
  • Functional groups: two amide-like carbonyls on the pyrimidinone ring; multiple secondary alcohols on the sugar; an N‑glycosidic bond joining base and sugar.
• 2D structure in words (general): a six-atom, conjugated pyrimidin-2,4-dione ring bearing a methyl at C5, attached at N1 to the anomeric carbon of an L‑ribofuranose ring (five‑membered), which carries hydroxyls at C2′, C3′, and a primary hydroxymethyl at C5′.
• Synonyms (literature): L‑ribothymidine; L‑5‑methyluridine; L‑(β)‑thymine riboside.

Synthetic Utility

L‑Thymine riboside is a versatile precursor for assembling L‑RNA and for preparing further modified L‑nucleoside analogs.

Key functional groups and reactivity (general literature guidance):

• 5′‑Primary alcohol: readily protected as 5′‑O‑DMT/MMTr to direct regioselectivity in further manipulations and to enable solid‑phase synthesis.
• 2′/3′‑Diol: protected as acetonide (isopropylidene) or silyl ethers (TBDMS, TIPDS) to control reactivity and prevent transesterification during phosphorylation.
• N3 of thymine: may be transiently protected (e.g., benzoyl) if conditions risk N‑alkylation; typically left unprotected for standard ribonucleoside chemistry.
• 5‑Methyl group: can be functionalized via radical halogenation or lithiation strategies to access C5‑substituted libraries (with care to avoid glycosidic cleavage).

Synthetic pathways:

• Phosphoramidite route: 5′‑O‑DMT protection, 2′/3′‑protection (e.g., TBDMS or TIPDS), followed by 3′‑ or 5′‑phosphitylation (chlorophosphoramidite reagents) affords amidites for automated L‑RNA synthesis.
• Phosphate esters: direct phosphorylation (POCl3/pyridine; phosphorimidazolide intermediates) to give mono-/di-/triphosphates for enzymology studies, noting many enzymes will not accept L‑substrates (by design).
• Conjugation: 5′‑ or 3′‑linked spacers (amines/azides/alkynes) enable post‑synthetic labeling or surface attachment for biosensor research.

Practical considerations:

• Ensure rigorous drying and use of anhydrous solvents to maximize yields in protection/phosphitylation.
• Maintain mild temperatures and avoid prolonged strong base/acid to preserve the N‑glycosidic bond and stereochemical integrity.

Target Specificity

Not applicable — this product is a small‑molecule nucleoside, not an antibody, enzyme, or affinity reagent. There are no item‑specific target, clone, isotype, or species‑reactivity attributes. For biochemical recognition studies, see the “Biological Roles” and “Reaction & Applications” sections.