This compound belongs to the class of organic compounds known as imidazole[4,5-c]pyridine ribonucleosides and ribonucleotides. These are organic compounds in which the C-1 of a ribosyl moiety is N-linked to an imidazole[4,5-c]pyridine ring system. Nucleotides have a phosphate group linked to the C5 carbon of the ribose (or deoxyribose) 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.
Certificati (CoA, COO, BSE/TSE e tabella di analisi)
C of A & Other Certificates(BSE/TSE, COO):
Analytical Chart:
Proprietà chimiche e fisiche
Peso molecolare
282.250 g/mol
XLogP3
-2.300
Hydrogen Bond Donor Count
5
Hydrogen Bond Acceptor Count
7
Rotatable Bond Count
2
Exact Mass
282.096 Da
Monoisotopic Mass
282.096 Da
Topological Polar Surface Area
143.000 Ų
Heavy Atom Count
20
Formal Charge
0
Complexity
445.000
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
Calcolatori di soluzioni
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Recensioni
Recensioni dei clienti
Application Protocols
No item-specific, tested application protocols are provided for this product. The following are general, literature-based suggestions for handling in common research contexts (verify and optimize empirically):
Preparation of stock solutions
Aqueous: Dissolve to 10–50 mM in nuclease-free water or buffer (pH 7–8). Gentle warming (≤37 C) and vortexing aid dissolution. Filter-sterilize (0.22 μm) if sterility is required.
DMSO: Prepare 50–200 mM stocks for solubility-limited assays; dilute into aqueous media to ≤1–2% DMSO final.
Quantification by UV
Record a spectrum (220–320 nm) and determine concentration using an empirically determined ε at the λmax; do not assume guanosine’s ε due to deaza substitution.
Standard phosphoramidite cycles apply; coupling times may be extended slightly if reactivity differs from canonical guanosine analogs. Deprotection conditions should be validated to preserve the deazapurine base.
LC–MS method development
Use a reversed-phase column (C18), water/acetonitrile with 0.1% formic acid or ammonium acetate for MS compatibility; monitor at ~260–270 nm and in positive ESI mode.
Biological Roles
Nature of the molecule (literature/general)
3-Deazaguanosine is a structural analog of guanosine in which the N3 ring nitrogen is replaced by carbon, altering hydrogen-bonding and protonation patterns. It is not a natural metabolite but is widely used as a biochemical probe.
Functional insights enabled by the analog (literature)
Base pairing: The missing N3 acceptor perturbs Watson–Crick geometry and Hoogsteen interactions, allowing evaluation of N3’s role in duplex stability and enzyme recognition.
Enzyme interactions: Changes in pKa/tautomer distribution affect binding and catalytic turnover in polymerases, kinases, and deaminases, illuminating recognition determinants without invoking therapeutic claims.
RNA structure/catalysis: Incorporated into ribozymes/aptamers to dissect active-site H-bond networks and metal-ion coordination indirectly via base electronics.
Analytical/biophysical uses
UV spectroscopic probe: Modified extinction coefficient relative to guanosine can be exploited to track incorporation or exchange when calibrated.
Thermodynamics: Differential scanning and melting analyses of oligonucleotides containing 3-deazaguanosine quantify contributions of the N3 position to duplex energetics (literature).
Note
For research use only (per Product Data). No medical or clinical claims are made.
Buffer Applications
This compound is not itself a buffering agent. It does not define a conventional buffer system or buffering range.
Practical guidance
Dissolve 3-deazaguanosine in an appropriate buffer selected for your assay (e.g., phosphate, HEPES, or Tris) based on enzyme or nucleic acid requirements.
Maintain neutral pH (≈6.5–8.0) to limit glycosidic bond cleavage; avoid strong acid/base unless required by the protocol (literature/general).
Green Alternatives
This product is a solid nucleoside rather than a volatile organic solvent; “green alternatives” primarily concern solvent choices and protecting-group strategies during use and synthesis (literature/general).
Greener dissolution media (use-phase)
Prefer water or aqueous buffers when feasible; use minimal DMSO as co-solvent. Avoid chlorinated solvents.
Use 2-MeTHF or CPME instead of THF/diethyl ether for moisture-sensitive protection steps when compatible.
Employ catalytic glycosylation methods (e.g., catalytic TMSOTf from bench-stable precursors) and reduce stoichiometric Lewis acids where possible.
Opt for greener protecting groups/removal conditions (e.g., carbonate or acetal protections removable under aqueous acid instead of hazardous HF for silyls).
Comparison (literature, qualitative)
Water vs DMSO: Water is safest/greenest; DMSO improves solubility but increases EHS burden; aim for ≤1–2% v/v DMSO in final aqueous systems.
CPME/2-MeTHF vs THF: Similar polarity with improved safety (lower peroxide formation, higher boiling point for CPME); check substrate compatibility.
Waste minimization
Use small-volume, high-concentration stocks to limit solvent use; quench and neutralize aqueous wastes per local regulations.
Pharmaceutical Uses
No excipient or pharmacopeial status is specified for this item; refer to the CoA/Spec Sheet.
Can serve as a reference standard or analytical control for method development involving modified nucleosides (e.g., LC–MS calibration).
As a building block, related protected derivatives (phosphoramidites) are used to prepare modified oligonucleotides for research and process development studies. This listing does not imply suitability for human or veterinary use.
Compliance note
For research use only (per Product Data). No claims are made regarding GMP manufacture, compendial compliance, or therapeutic application.
Physical Properties
Item-specific physical data
Appearance: Not specified for this item; refer to CoA/Spec Sheet.
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Density, refractive index, UV cutoff: Not specified for this item; refer to CoA/Spec Sheet.
Literature/general characteristics (not item-specific; typical for 3-deazaguanosine and related nucleosides)
Physical state: Solid, crystalline powder; highly polar due to multiple hydroxyls and heteroatoms.
Melting point: Often >200 C (many nucleosides decompose on melting); precise MP for this specific analog is not cited here (literature).
Solubility: Readily soluble in water and aqueous buffers; soluble in polar aprotic solvents (DMSO, DMF); sparingly soluble in lower alcohols; negligible solubility in nonpolar solvents (literature).
UV absorption: Nucleoside-like π→π* band with λmax typically in the 250–280 nm region; 3-deazapurine substitution may red/blue-shift relative to guanosine; verify experimentally (literature).
pKa: Replacement of N3 (a ring N) with carbon reduces basicity relative to guanosine; net acid–base behavior dominated by the exocyclic amino and ring keto tautomerism; numeric pKa values vary by source (literature).
LogP/LogD: Strongly hydrophilic; expected negative logP; distribution depends on ionization state (literature).
Practical notes
Prepare aqueous stocks fresh or store frozen to prevent slow hydrolysis/oxidation. Measure concentration by UV using an empirically determined ε for the batch (literature best practice).
Quality and Grades
Item-specific quality attributes
Grade/Purity: Not specified for this item; refer to CoA/Spec Sheet.
Stabilizers/additives: Not specified for this item; refer to CoA/Spec Sheet.
What grade implies (general guidance)
Research/biochemical grade for nucleosides typically indicates high chemical purity (often ≥95–98% by HPLC), low inorganic residue, and low UV-absorbing impurities to ensure reproducible spectrophotometric quantification (literature/general).
For oligonucleotide synthesis use, additional specifications may include water content (KF), residual solvents, and isomeric purity (α/β anomer ratio). None are specified here for this item; consult the CoA if critical to your application.
Fit-for-purpose checks (recommended best practices)
Verify identity by 1H/13C NMR and HRMS; confirm β-anomer content if relevant to enzymatic incorporation studies.
Assess purity by HPLC with UV detection near the compound’s λmax; evaluate for deprotected sugar impurities and ring-opened species.
If using enzymatically, test background absorbance and pH-dependent stability of stock solutions before committing critical samples.
Reaction and Applications
Research applications (literature/general for 3-deazaguanosine)
Structural probe: Substitution of N3 with carbon removes a ring nitrogen H-bond acceptor, enabling dissection of guanine N3 roles in base pairing, catalysis, and ligand recognition in RNA and enzymes.
Enzymology: Used to study substrate recognition and catalysis by nucleoside kinases, deaminases, and polymerases; altered pKa/tautomerism can change binding/incorporation kinetics (no clinical claims).
Nucleic acid chemistry: Incorporated into RNA/DNA oligonucleotides (via corresponding phosphoramidites) to tune duplex stability and study Hoogsteen/Watson–Crick pairing energetics.
Chemical transformations (literature)
Protection of 2′,3′-diol (e.g., as acetonide or silyl ethers) and 5′-OH (e.g., DMT) enables subsequent derivatization.
Conversion to 5′-O-DMT-3′-O-(phosphoramidite) allows automated solid-phase synthesis of modified oligonucleotides.
Base functionalization at C8 and exocyclic positions follows purine chemistry with adjustments for the deazapurine ring electronics.
Practical considerations
Sensitive functionalities: Avoid prolonged strong acid/base in solution; monitor reactions by HPLC.
Quantification: Determine extinction coefficient experimentally for accurate dosing since 3-deaza substitution shifts UV response relative to guanosine (literature).
Reaction Conditions
General literature guidance for nucleoside chemistry involving 3-deazaguanosine or its protected derivatives (not item-specific; verify experimentally):
Glycosylation (formation of the nucleoside)
Conditions: Vorbrüggen protocol; silylate base with HMDS/TMSCl; couple with peracylated ribose donor using TMSOTf (0.5–1.5 eq) in dry dichloroethane or acetonitrile at 0–25 C for 1–6 h. Typical isolated yields: 40–75% depending on substrate and protection.
Protection/deprotection
5′-O-DMT: DMTCl, pyridine/DMAP, 0–25 C, 1–3 h; remove with 3% TCA in DCM or 80% acetic acid (minutes).
2′-O-TBDMS (RNA): TBDMS-Cl, imidazole, DMF, 25 C, 4–16 h; remove with TBAF or HF·pyridine (monitor to avoid base/sugar cleavage).
Reagents: 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, DIPEA, DCM or THF, 0–25 C, 0.5–2 h; protect from moisture; typical yields 70–90% (literature).
C8 functionalization
Halogenation: NBS/NIS in DMF or AcOH, 0–25 C; follow with Suzuki or Sonogashira using Pd catalysts under standard conditions.
Analysis and workup
Monitor by HPLC (UV 254–270 nm) and TLC (visualize with UV). Avoid strong base at elevated temperature to prevent glycosidic cleavage.
Safety and Handling
GHS/SDS information (item-specific)
Signal word, H-statements, pictograms, and classification: Not specified for this item; refer to the SDS.
Research Use: For research use only (non-clinical, non-diagnostic).
General laboratory handling (literature/guidance for nucleosides)
Hazards: Typically low acute toxicity; may cause irritation to eyes/skin/respiratory tract if dust is generated. Avoid ingestion and inhalation of powders.
PPE: Lab coat, safety glasses, and suitable gloves (e.g., disposable nitrile). Use dust control (weighing in fume hood) for fine powders.
Hygiene: Wash hands after handling. Do not eat, drink, or smoke in lab areas. Avoid creating aerosols.
First aid (overview; defer to SDS)
Inhalation: Move to fresh air; seek medical advice if symptoms persist.
Skin contact: Wash with soap and water; remove contaminated clothing.
Eye contact: Rinse cautiously with water for several minutes; remove contact lenses if present and easy; seek attention if irritation continues.
Ingestion: Rinse mouth; do not induce vomiting unless directed by medical personnel.
Incompatibilities: Strong oxidizers can degrade nucleosides; strong acids/bases can promote glycosidic bond cleavage or sugar dehydration (literature).
Environmental: Avoid release to the environment; dispose according to institutional and local regulations.
Storage conditions
Item-specific: Room temperature (per Product Data). Store tightly capped in a dry, well-ventilated place; protect from prolonged light exposure (good practice).
Solvent Selection
Polarity and miscibility profile (literature/general)
Highly polar, hydrogen-bonding solid; dissolves well in water and aqueous buffers.
Good solubility in DMSO and DMF; moderate in formamide; limited in methanol/ethanol; negligible in acetone, acetonitrile (without water), and nonpolar media.
Choosing a vehicle
Aqueous biology/biochemistry: Use nuclease-free water or buffer (e.g., phosphate, Tris) adjusted to application pH; filter-sterilize if sterility required.
Chemical manipulations: Use DMSO or DMF for higher-concentration stocks; co-solvent strategies (water/DMSO) enable accurate dosing in assays (literature).
Practical comparison (literature)
Water: Greenest, compatible with spectrophotometry; limited by hydrolytic stability at extreme pH.
DMSO: Excellent solubilizer; compatible with most bioassays at ≤1–2% v/v final; hygroscopic.
Methanol/Ethanol: May be inadequate for high concentrations; can participate in acyl/alkyl exchange in protected derivatives.
Tips
Warm gently (≤37 C) and vortex to assist dissolution. Avoid strong base or acid unless intended, as nucleosides can undergo glycosidic cleavage under harsh conditions (literature).
Storage and Reconstitution
Storage conditions (item-specific)
Store at room temperature (per Product Data). Keep container tightly closed in a dry place. Protect from prolonged exposure to light and ambient humidity.
Stability (general/literature)
Solid nucleosides are typically stable for months to years when kept dry and protected from heat and light. In solution, stability decreases with extreme pH and temperature; neutral pH and cold storage slow degradation.
Reconstitution guidance (general)
Solvents: Water, buffer (pH 6.5–8.0), or DMSO.
Procedure: Bring solid to room temperature in a desiccator, then weigh quickly to minimize moisture uptake. Add solvent gradually with vortexing; warm gently (≤37 C) if needed. Filter sterilize for cell-free enzymology.
Working aliquots: Prepare single-use aliquots to avoid repeated freeze–thaw.
Solution storage (general)
Aqueous solutions: Store at 2–8 C for short term (≤1 week) or at −20 C for longer term; avoid multiple freeze–thaw cycles.
DMSO stocks: Store at −20 C, desiccated and protected from light; equilibrate to room temperature before opening to prevent moisture condensation.
Shipping
Shipped condition: Not specified for this item; refer to CoA/Spec Sheet.
Structure and Identity
Brief overview: 3-Deazaguanosine is a guanosine analog in which the N3 of the purine ring is replaced by carbon (a 3-deazapurine nucleoside) attached to β-D-ribofuranose.
Item-specific identifiers (from Product Data)
SKU: D990239
Product name: 3-Deazaguanosine
CAS: 56039-11-3
Storage: Room temperature
InChIKey: Not specified for this item; refer to CoA/Spec Sheet.
SMILES: Not specified for this item; refer to CoA/Spec Sheet.
Literature/computed identity (general reference; not item-specific)
Core scaffold: 3-deazapurine (a purine analog with a fused imidazole–pyrimidine ring system where N3 is replaced by C–H) linked at the “N9/C9” position to β-D-ribofuranose.
Molecular formula (literature): C11H14N4O5
Molecular weight (literature): ~282.26 g/mol; monoisotopic mass ~282.0964 Da
Structural features: Ribofuranose bearing 2′,3′,5′-hydroxyls; base contains keto and amino functions akin to guanine but with altered ring nitrogen count (N3→C). No stereocenters in the base; D-ribose has standard β-configuration at the anomeric center.
2D description in words
A five-membered ribose ring (furanose) with free hydroxyls at C2′, C3′, and a primary OH at C5′; the anomeric C1′ is β-linked to the deazapurine base. The base resembles guanine but with N3 replaced by carbon, retaining a C6 carbonyl and a C2 exocyclic amino group (literature).
Synthetic Utility
Functional groups and handles (literature/general)
Polyol (2′,3′,5′-OH) on ribose enables orthogonal protection: acetonide, silyl (TBDMS/TBS), benzoyl/acetyl; 5′-O-DMT for oligo synthesis.
Base features a C6 carbonyl and C2 exocyclic amino group; C8 can undergo electrophilic substitution; deazapurine ring electronics differ from purine, affecting regioselectivity.
Key transformations
Preparation of phosphoramidites: Protect 5′-OH with DMT, mask 2′-OH (RNA) with TBDMS or TOM, convert 3′-OH to 2-cyanoethyl N,N-diisopropyl phosphoramidite under mild base (DIPEA) (literature).
Vorbrüggen-type glycosylation: Generation of the nucleoside from the silylated 3-deazaguanine base with an activated ribose donor (e.g., 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose) catalyzed by TMSOTf or SnCl4; β-selectivity managed by neighboring group participation (literature).
Late-stage base modification: N2 acylation/carbamate formation; C8 halogenation (NBS/NCS) followed by cross-coupling to diversify.
Retrosynthetic value
Breaks into base and sugar components, enabling modular access to analog series (altered sugars, different protecting groups) for SAR in nucleic acids research.
Target Specificity
Not applicable. This product is a small-molecule nucleoside, not an antibody or targeted biological. No antigen/epitope, clone, isotype, or species reactivity data apply.
Domande frequenti
What is the purity of this product?
This product is supplied at ≥95% purity (chemical assay). Lot-specific values are stated on the Certificate of Analysis.
How should this product be stored?
Store at room temperature.
What are the CAS number, molecular formula and molecular weight?
The CAS Number is 56039-11-3, the molecular formula is C11H14N4O5, and the molecular weight is 282.25 g/mol. InChIKey JJXPEDPBLSOWRJ-MGUDNFKCSA-N.
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.
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