2-Deoxy-D-ribose — The DNA Sugar, ≥99% HPLC, Biochemical Reagent & Pharmaceutical Intermediate Grade Supplier
2-Deoxy-D-ribose (CAS 533-67-5) is the defining carbohydrate component of deoxyribonucleic acid — the pentose sugar that forms the backbone of DNA in all living organisms. Its critical structural feature, the absence of the 2′-hydroxyl group (replaced by hydrogen), confers the chemical stability that makes DNA suitable for long-term genetic information storage, distinguishing it fundamentally from the more labile RNA. At ≥99% HPLC purity, UPOR Biotech’s 2-deoxy-D-ribose meets the exacting standards required for nucleoside phosphoramidite synthesis, antiviral drug intermediate production, and advanced biotechnology research applications worldwide.
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2-Deoxy-D-ribose is a five-carbon aldopentose that serves as the carbohydrate backbone of deoxyribonucleic acid (DNA), wherein each nucleotide incorporates a 2-deoxy-D-ribofuranose moiety linked via an N-glycosidic bond to a nucleobase and connected through 3′-5′ phosphodiester linkages to form the iconic double-helical polymer. The defining molecular feature — and the etymological origin of the “deoxy” prefix — is the replacement of the 2′-hydroxyl group present in D-ribose with a single hydrogen atom at C-2, a substitution that eliminates the intramolecular nucleophilic catalyst responsible for RNA’s susceptibility to base-catalyzed strand cleavage via the 2′,3′-cyclic phosphate intermediate. This chemical stabilization is the evolutionary rationale for Nature’s selection of 2-deoxy-D-ribose over ribose as the sugar component of the primary genetic information repository, ensuring that the blueprint of life remains intact across cellular generations. In the solid state, 2-deoxy-D-ribose crystallizes as a white to off-white powder exhibiting mutarotation in aqueous solution — a dynamic equilibrium between the α-furanose and β-furanose anomers via the open-chain aldehyde form — with an equilibrium specific rotation of approximately −58 degrees. The compound is freely soluble in water and polar organic solvents, displays a well-defined melting point of 89–91°C, and serves as an indispensable chiral synthon for the construction of modified nucleoside analogs, antisense oligonucleotides, and antiviral therapeutics including stavudine (d4T), didanosine (ddI), and zidovudine (AZT). UPOR Biotech supplies 2-deoxy-D-ribose at ≥99.0% HPLC purity under c-GMP conditions, with comprehensive analytical documentation supporting its use from early-stage medicinal chemistry through commercial API manufacture.
As a leading biochemical reagent and pharmaceutical intermediate supplier, UPOR Biotech delivers 2-deoxy-D-ribose to research institutions, biotechnology firms, and pharmaceutical manufacturers across North America, Europe, and Asia-Pacific. Our product is manufactured under an ISO 9001:2015-certified quality management system with full traceability from raw material sourcing through final packaging, ensuring lot-to-lot consistency for critical applications including DNA research, cell culture supplementation, diagnostic reagent formulation, and cosmetic anti-aging actives. Each batch is accompanied by a comprehensive Certificate of Analysis (CoA), Material Safety Data Sheet (MSDS), and GMP compliance statement, with additional regulatory support documentation (Drug Master File access, residual solvent profiles, elemental impurity data per ICH Q3D) available under confidentiality agreement. With HALAL and KOSHER certifications complementing our technical quality credentials, UPOR Biotech’s 2-deoxy-D-ribose is positioned to support the full spectrum of life science applications from fundamental nucleic acid biochemistry to commercial pharmaceutical production.
🧬 The Carbohydrate of Life — 2-Deoxy-D-ribose at the Heart of DNA
Every nucleotide in the DNA double helix — whether bearing adenine, thymine, guanine, or cytosine — is built upon a 2-deoxy-D-ribose scaffold. The absence of the 2′-OH group, nature’s elegantly simple chemical modification, renders DNA approximately 100-fold more resistant to hydrolytic degradation than RNA under physiological conditions. This single atom substitution — oxygen replaced by hydrogen — is the molecular basis for DNA’s role as the stable archive of genetic information, enabling genomes to persist across millennia. At UPOR Biotech, we honor this profound biochemistry by supplying 2-deoxy-D-ribose at the purity and quality that modern nucleic acid science demands.
Technical Specifications
| Product Name | 2-Deoxy-D-ribose |
|---|---|
| Synonyms | Thyminose; 2-Deoxy-D-erythro-pentose; 2-Deoxy-D-arabinose; D-2-Deoxyribose; 2-Deoxy-β-D-ribose; 2-Deoxy-D-ribofuranose |
| CAS Number | 533-67-5 |
| Molecular Formula | C₅H₁₀O₄ |
| Molecular Weight | 134.13 g/mol |
| Appearance | White to off-white crystalline powder |
| Key Feature | The carbohydrate component of DNA — 2-deoxy-D-ribose forms the sugar-phosphate backbone of deoxyribonucleic acid. The critical structural distinction from D-ribose (the RNA sugar) is the absence of the 2′-OH group (replaced by 2′-H), which renders DNA chemically more stable than RNA by eliminating the base-catalyzed intramolecular hydrolysis mechanism (2′-OH attack on adjacent phosphodiester → 2′,3′-cyclic phosphate → strand scission). This single atomic substitution — oxygen for hydrogen at C-2 — is the molecular basis for DNA’s role as the stable, long-term repository of genetic information. |
| Melting Point | 89–91°C |
| Specific Rotation | [α]D²⁰ = −55° to −60° (c=1, H₂O, equilibrium); mutarotation occurs — initial [α]D = −55° (α-anomer) shifting to ~−58° at equilibrium over 2–4 hours at 25°C |
| Assay (HPLC) | ≥99.0% (typical 99.2–99.8%) |
| Related Substances | Total impurities ≤0.5%; any single impurity ≤0.2% (HPLC, 210 nm) |
| Water Content (Karl Fischer) | ≤0.5% |
| Solubility | Freely soluble in water (>100 mg/mL at 25°C); soluble in methanol, ethanol; slightly soluble in acetone; practically insoluble in diethyl ether, chloroform, hexane |
| pH (Aqueous Solution) | 4.5–6.5 (1% solution in water at 25°C) |
| Loss on Drying | ≤1.0% (60°C, vacuum, 4 hours over P₂O₅) |
| Ash Content (Sulfated) | ≤0.1% |
| Heavy Metals | ≤10 ppm (as Pb) |
| Total Plate Count | ≤100 CFU/g |
| Yeast & Mold | ≤10 CFU/g |
| E. coli / Salmonella / S. aureus | Absent in 1 g / Absent in 25 g / Absent in 1 g |
| Endotoxins | ≤0.25 EU/mg (for pharmaceutical intermediate and cell culture grades) |
| Recommended Storage | Store at +2°C to +8°C in a tightly sealed container under inert atmosphere (argon or nitrogen), protected from light and moisture. Long-term storage recommended at −20°C under argon. |
| Grade | Biochemical Reagent Grade / Research Grade / Pharmaceutical Intermediate Grade |
| Certifications | ISO 9001:2015, c-GMP, HALAL, KOSHER |
| Packaging | 1 g, 5 g, 10 g, 25 g, 100 g, 500 g, 1 kg, 5 kg, 25 kg (custom packaging available upon request; pharmaceutical grade supplied in LDPE double-bagged, foil-sealed, argon-flushed containers) |
| Shelf Life | 36 months from date of manufacture when stored under recommended conditions; retest after 36 months |
Key Benefits & Mechanisms
The DNA Sugar — Absence of 2′-OH Confers Chemical Stability Critical for Genetic Information Storage
The defining molecular feature of 2-deoxy-D-ribose — the replacement of the 2′-OH group with a hydrogen atom — is far more than a trivial structural distinction: it is the chemical basis for DNA’s biological function as the stable archive of heredity. In RNA, the 2′-OH group acts as an intramolecular nucleophile poised to attack the adjacent 3′-phosphodiester linkage. Under mildly basic conditions (pH >7), the 2′-alkoxide ion (generated by deprotonation of the 2′-OH, pKa ~12.5) executes a transesterification reaction, cleaving the RNA backbone and generating a 2′,3′-cyclic phosphate intermediate with concomitant release of a 5′-OH terminus. This hydrolysis pathway, catalyzed by hydroxide ion, general bases, or ribonucleases, means RNA is inherently transient — suitable for messenger and regulatory functions but ill-suited for permanent information storage. DNA, by substituting 2′-H for 2′-OH, eliminates this degradation mechanism entirely. The result: DNA is approximately 100-fold more stable than RNA under physiological conditions, enabling genomes to persist intact across cellular generations and, under favorable conditions, for tens of thousands of years. This elegant evolutionary solution — a single atomic substitution — is why 2-deoxy-D-ribose is the carbohydrate scaffold of the molecule of heredity.
High Purity (≥99% HPLC) — Reliable Starting Material for Nucleoside Phosphoramidite Synthesis
The synthesis of nucleoside phosphoramidites — the gold-standard building blocks for solid-phase oligonucleotide synthesis — demands exceptionally pure 2-deoxy-D-ribose as starting material. Impurities at even the 0.5% level can generate byproducts that propagate through multi-step synthetic sequences, compromising yields during Vorbruggen glycosylation (silylated nucleobase coupling with 1-O-acetyl-2-deoxy-3,5-di-O-toluoyl-D-ribofuranose), selective protection/deprotection of the 3′- and 5′-hydroxyl groups, and final phosphitylation to install the 3′-O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite moiety. UPOR Biotech’s ≥99.0% HPLC purity specification — with typical batch purity reaching 99.5% or higher — ensures that medicinal chemists and process development scientists can execute these sensitive transformations with predictable reaction kinetics and high diastereomeric purity at the anomeric center. This purity level also supports enzymatic transglycosylation reactions using purine nucleoside phosphorylase (PNP) or thymidine phosphorylase (TP) for the biocatalytic synthesis of modified nucleosides, where trace inhibitors can reduce turnover numbers by orders of magnitude.
Mutarotation Behavior — Understanding the α/β-Anomer Equilibrium for Reproducible Formulation
In aqueous solution, 2-deoxy-D-ribose exists as a dynamic equilibrium mixture of the α-furanose (axial C-1 OH), β-furanose (equatorial C-1 OH), α-pyranose, β-pyranose, and open-chain aldehyde forms, interconverting via the ring-opening/ring-closing tautomerism known as mutarotation. Freshly dissolved crystalline 2-deoxy-D-ribose (predominantly the α-anomer in the solid state) exhibits an initial specific rotation of approximately [α]D = −55°, which gradually shifts toward the equilibrium value of ~−58° over 2–4 hours at 25°C as the β-anomer accumulates. For applications where anomeric composition affects reactivity — including enzymatic assays (ribokinase, deoxyribose-5-phosphate aldolase), chemical glycosylation reactions with stereochemical preferences, and NMR spectroscopic analyses where α/β anomer signals must be correctly assigned — solutions should be equilibrated prior to use. UPOR Biotech recommends preparing aqueous stock solutions at least 4 hours before critical experiments and storing them at 4°C to slow re-equilibration. For lyophilized formulations or solid-dosage pharmaceutical preparations, the mutarotation equilibrium is arrested upon drying, and the anomeric composition of the final product reflects the equilibrium in the solution from which it was lyophilized.
Natural Configuration (D-erythro-pentose) — Identical to Human DNA Sugar for Biocompatibility
2-Deoxy-D-ribose as supplied by UPOR Biotech possesses the natural D-erythro stereochemical configuration — the identical enantiomeric form found in human DNA and the DNA of all terrestrial organisms. The D-configuration at C-4 (R-configuration in the Fischer projection) establishes the absolute stereochemistry that is recognized by every enzyme in nucleotide metabolism: deoxyribokinase for the initial 5-phosphorylation, phosphoribosylpyrophosphate (PRPP) synthetase for phosphoribosyl transfer, ribonucleotide reductase for the de novo deoxyribonucleotide pathway, and the entire DNA replication and repair machinery. The use of the natural D-enantiomer ensures full biocompatibility — the compound is metabolized through endogenous pathways, incorporated correctly into synthetic oligonucleotide therapeutics, and recognized by cellular enzymes without the chiral discrimination issues that plague unnatural L-enantiomers. This stereochemical fidelity is critical for pharmaceutical applications: nucleoside analog prodrugs (e.g., tenofovir disoproxil fumarate precursors, investigational antisense oligonucleotides) rely on the correct D-configuration for efficient enzymatic activation by cellular kinases and for proper base-pairing geometry within the DNA double helix. UPOR Biotech confirms enantiomeric purity by chiral HPLC and specific rotation measurement for every production batch.
Applications
Nucleoside & Nucleotide Synthesis
2-Deoxy-D-ribose is the fundamental chiral pool starting material for the chemical synthesis of natural and modified 2′-deoxynucleosides. The classical Vorbruggen glycosylation — condensation of silylated nucleobases (thymine, N-benzoyl-adenine, N-acetyl-cytosine, N-isobutyryl-guanine) with 1-O-acetyl-2-deoxy-3,5-di-O-toluoyl-D-ribofuranose in the presence of a Lewis acid catalyst (SnCl₄ or TMSOTf) — proceeds with high β-stereoselectivity due to anchimeric assistance from the 2-acyl protecting group. This chemistry underpins the manufacture of DNA building blocks for solid-phase oligonucleotide synthesis and the production of nucleoside analog active pharmaceutical ingredients. The 2-deoxy configuration at C-2 is preserved throughout the synthetic sequence, ensuring that the final nucleoside product retains the correct stereochemistry for biological activity.
Antiviral Drug Intermediate
2-Deoxy-D-ribose is the essential carbohydrate precursor for the synthesis of nucleoside reverse transcriptase inhibitors (NRTIs) — the cornerstone of antiretroviral therapy for HIV and hepatitis B. Clinically approved drugs derived from 2-deoxy-D-ribose or its modified analogs include stavudine (d4T), didanosine (ddI), zidovudine (AZT), lamivudine (3TC), emtricitabine (FTC), and abacavir. The synthetic routes typically involve selective protection of the sugar hydroxyls, introduction of the nucleobase via glycosylation, and modification of the sugar moiety (e.g., 2′,3′-didehydro-2′,3′-dideoxy elimination for stavudine; 2′,3′-dideoxy reduction for didanosine). UPOR Biotech supplies pharmaceutical intermediate grade 2-deoxy-D-ribose with documentation supporting Drug Master File (DMF) filings and regulatory submissions.
DNA Research & Biotechnology
In fundamental nucleic acid biochemistry, 2-deoxy-D-ribose is used to study DNA repair mechanisms (base excision repair, nucleotide excision repair), deoxyribonucleotide metabolism (ribonucleotide reductase, thymidylate synthase, dihydrofolate reductase pathways), and DNA-protein interactions (transcription factor binding, histone-DNA contacts). It serves as a substrate for deoxyribose-5-phosphate aldolase (DERA) — the key enzyme in the reversible aldol cleavage of 2-deoxy-D-ribose-5-phosphate to acetaldehyde and D-glyceraldehyde-3-phosphate — an enzyme exploited industrially for the stereoselective synthesis of chiral lactol intermediates for statin drugs. Radiolabeled and stable-isotope-labeled 2-deoxy-D-ribose (¹⁴C, ¹³C, ²H) prepared from our high-purity material enables tracer studies of deoxyribonucleotide flux in cell culture and in vivo models.
Cell Culture Supplement
2-Deoxy-D-ribose is employed as a media supplement in specialized mammalian and bacterial cell culture systems where modulation of deoxyribonucleotide pools is required. In genetic toxicology and cancer biology research, it is used to study the effects of deoxyribonucleotide pool imbalances on DNA replication fidelity, mutagenesis rates, and cellular responses to replication stress (ATR/CHK1 pathway activation). In in vitro toxicology, 2-deoxy-D-ribose is a component of the deoxyribose degradation assay for hydroxyl radical detection. For industrial biotechnology, it serves as a carbon source and precursor for engineered microbial strains producing modified nucleosides through metabolic engineering of the pentose phosphate and deoxyribonucleotide pathways.
Diagnostic Reagent
2-Deoxy-D-ribose and its derivatives are essential components in molecular diagnostics, including the formulation of PCR master mixes, DNA sequencing reagents, and microarray hybridization buffers. The compound serves as a reference standard for HPLC and LC-MS/MS methods quantifying deoxyribonucleosides in biological fluids (plasma, urine, cerebrospinal fluid) for the diagnosis of inherited disorders of purine and pyrimidine metabolism (e.g., purine nucleoside phosphorylase deficiency, thymidine phosphorylase deficiency — MNGIE syndrome). It is also used in enzymatic assay kits for deoxyribose-5-phosphate aldolase (DERA) activity measurement in clinical and research settings, and as a calibrant for polarimetric and refractometric detectors in HPLC systems analyzing carbohydrate mixtures.
Cosmetic Active (Anti-Aging)
Emerging research has positioned 2-deoxy-D-ribose as a novel anti-aging cosmetic active with a mechanism distinct from conventional antioxidants and retinoids. 2-Deoxy-D-ribose stimulates cellular NAD⁺ biosynthesis via the salvage pathway, enhancing sirtuin (SIRT1, SIRT3) activity and promoting mitochondrial biogenesis and DNA repair capacity in dermal fibroblasts and epidermal keratinocytes. Topical formulations containing 2-deoxy-D-ribose have demonstrated improved skin elasticity, reduced appearance of fine lines, and enhanced barrier function recovery in ex vivo human skin explant models and pilot clinical studies. As a naturally occurring metabolite already present in human cells, 2-deoxy-D-ribose offers an excellent safety and tolerability profile for cosmetic applications. UPOR Biotech supplies cosmetic-grade 2-deoxy-D-ribose meeting the purity and microbiological specifications required for topical formulation development.
Frequently Asked Questions
2-Deoxy-D-ribose is a five-carbon monosaccharide (pentose) and the carbohydrate backbone of deoxyribonucleic acid (DNA). It is called the “DNA sugar” because every nucleotide in DNA contains a 2-deoxy-D-ribose residue linked via N-glycosidic bonds to purine or pyrimidine bases and connected through 3′-5′ phosphodiester linkages to form the DNA polymer. The term “deoxy” refers to the replacement of the 2′-OH group found in ribose with a hydrogen atom, making it the defining molecular feature that distinguishes DNA from RNA. Discovered by Phoebus Levene in 1929 during his pioneering studies on nucleic acid structure, 2-deoxy-D-ribose was identified as the sugar component liberated upon acid hydrolysis of thymus DNA (hence the synonym “thyminose”). Its D-erythro stereochemical configuration — identical in all organisms across all domains of life — reflects the universal evolutionary origin of DNA as the molecule of heredity.
The sole structural difference is at the C-2 position: D-ribose bears a hydroxyl group (2′-OH), while 2-deoxy-D-ribose bears a hydrogen atom (2′-H). This single substitution has profound biochemical consequences. The 2′-OH in RNA acts as an intramolecular nucleophile, attacking the adjacent phosphodiester bond under basic conditions to form a 2′,3′-cyclic phosphate intermediate, leading to strand cleavage. DNA, lacking this 2′-OH, is resistant to this base-catalyzed hydrolysis mechanism, conferring the chemical stability essential for long-term genetic information storage across generations. Quantitatively, the rate of alkaline hydrolysis of RNA is approximately 10¹–10² times faster than that of DNA at pH 7.4 and 37°C. Beyond stability, the 2′-H in DNA also alters sugar pucker conformation — DNA favors the C-2′-endo conformation (B-form helix), while RNA with its 2′-OH favors the C-3′-endo conformation (A-form helix) — with ramifications for double helix geometry, protein recognition, and the catalytic activity of ribozymes.
2-Deoxy-D-ribose is a critical building block for nucleoside and nucleotide synthesis, serving as the starting material for antiviral drugs (e.g., stavudine, didanosine, zidovudine) and antisense oligonucleotides. In biotechnology, it is used in DNA research, cell culture media supplementation, and diagnostic reagent formulation. It also serves as a pharmaceutical intermediate for modified nucleoside analogs, and finds emerging use in cosmetic anti-aging formulations due to its role in cellular energy metabolism and DNA repair pathway signaling. In enzymatic biotechnology, 2-deoxy-D-ribose-5-phosphate (the phosphorylated derivative) is the substrate for deoxyribose-5-phosphate aldolase (DERA), an enzyme exploited for the industrial synthesis of chiral intermediates for statin drugs through stereoselective aldol reactions. The compound is also essential in the development of therapeutic oligonucleotides — including antisense, siRNA, aptamer, and CRISPR guide RNA technologies — where 2′-deoxy building blocks provide the structural foundation for nuclease-resistant, backbone-modified oligonucleotide drugs.
Mutarotation is the spontaneous interconversion between the α- and β-anomers of 2-deoxy-D-ribose in aqueous solution via the open-chain aldehyde intermediate. The initial specific rotation of [α]D = −55° (predominantly α-anomer) gradually shifts to approximately −58° at equilibrium as the α/β ratio stabilizes. For reproducible formulation, solutions should be allowed to equilibrate (typically 2-4 hours at room temperature) before use in critical applications such as enzymatic assays, glycosylation reactions, or spectroscopic measurements where anomeric composition affects reactivity and optical properties. The mutarotation rate is pH-dependent, accelerating under both acidic and basic catalysis; at pH 7.0 and 25°C, the half-time for equilibration is approximately 30–45 minutes. For pharmaceutical formulations, the anomeric equilibrium is typically “locked” by lyophilization or spray-drying — the solid-state form preserves the equilibrium anomeric ratio present in the solution at the moment of drying. UPOR Biotech’s Certificates of Analysis report the equilibrium specific rotation to ensure that customers receive material with defined, reproducible anomeric composition.
UPOR Biotech supplies 2-deoxy-D-ribose at ≥99.0% HPLC purity (Biochemical Reagent Grade, Research Grade, and Pharmaceutical Intermediate Grade) with full documentation. Certifications include ISO 9001:2015, c-GMP, HALAL, and KOSHER. Each shipment includes a comprehensive Certificate of Analysis (CoA) detailing assay (HPLC), specific rotation, water content (Karl Fischer), loss on drying, residue on ignition, heavy metals, and microbiological limits. A Material Safety Data Sheet (MSDS/SDS) and a GMP Statement of Compliance are also provided. Additional documentation for regulatory filings (Drug Master File letter of access, residual solvent profile, elemental impurities per ICH Q3D) is available under a Confidential Disclosure Agreement. Our quality control laboratory employs validated pharmacopoeial and in-house methods including HPLC-UV/RI, Karl Fischer coulometry, ICP-MS for elemental impurities, and compendial microbial limits testing per USP <61> and <62>. Third-party stability studies (ICH Q1A: 25°C/60% RH long-term, 40°C/75% RH accelerated) are available for pharmaceutical intermediate grade material to support shelf-life assignment and regulatory dossier compilation.