DMT-dG(dmf) Phosphoramidite - Moligand™, 10 mM in DMSO , CAS No.330628-04-1

CAS: 330628-04-1 Cat. No.: D1496683 Formula: C₄₃H₅₃N₈O₇P Peso molecolare: 824.90 PubChem CID: 136334904

GRADE & PURITY Moligand™, 10 mM in DMSO

Storage

Protected from light,Store at -80°C

Shipped In

Dry ice packs + Cold packs

Panoramica

DMT-dG(dmf) Phosphoramidite is a phosphinamide monomer that can be used in the preparation of oligonucleotides

Specifications

Specifiche e purezza

Moligand™, 10 mM in DMSO

Condizioni di conservazione di stoccaggio

Protected from light,Store at -80°C

Spedito in

Dry ice packs + Cold packs

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Grado

Moligand™

Nomi e identificatori

• PubChem CID: 136334904
• Peso molecolare: 824.90

Application Protocols

General protocol outline for preparing and using DMT-dG(dmf) Phosphoramidite on an automated DNA synthesizer (literature/practice; adjust to your platform):

• Reagent preparation:
  • Bring container to room temperature in a desiccator before opening to avoid moisture condensation.
  • In a dry box or under inert gas, dissolve the amidite to 0.1 M in anhydrous MeCN. Filter through a dry 0.2 µm PTFE filter if particulates are present.
  • Charge the synthesizer bottle, backfill headspace with argon/nitrogen, and cap tightly.
• Instrument setup:
  • Load compatible activator (e.g., 0.25–0.45 M ETT in MeCN), capping solutions, and oxidizer per instrument SOP.
  • Prime lines to remove air and ensure anhydrous conditions.
• Synthesis cycle (typical):
  1. Detritylation of support-bound 5′-OH.
  2. Coupling with amidite/activator for the validated time.
  3. Capping of unreacted 5′-OH.
  4. Oxidation (or sulfurization) of the phosphite linkage.
  5. Repeat steps for subsequent residues; final detritylation as required.
• Post-synthesis:
  • Cleave and deprotect under conditions suitable for dmf-protected G and your support (e.g., NH4OH or AMA).
  • Purify by RP-HPLC or cartridge methods; analyze by LC–MS and analytical HPLC.

Item-specific tested applications or dilutions: Not specified for this item; refer to CoA/Spec Sheet.

Biological Roles

Context (general biochemistry; not a product specification):

• Guanine is one of the four canonical nucleobases in DNA, pairing with cytosine via three hydrogen bonds to stabilize the double helix.
• 2′-Deoxyguanosine units contribute to sequence-specific recognition by proteins (e.g., transcription factors) and influence DNA structure in G-rich regions (e.g., G-quadruplex motifs).
• Chemical protection (DMT at 5′-O, dmf on guanine exocyclic amine) is temporary and removed post-synthesis to regenerate native DNA. These protecting groups have no biological role in final oligonucleotides.
• Post-synthetic deprotection typically restores the guanine amino functionality, enabling normal Watson–Crick base pairing and participation in enzymatic processes if the oligonucleotide is subsequently used in biochemical assays.

Important boundaries:

• This product is intended for research and laboratory synthesis of oligonucleotides only. It is not intended for use in humans or for diagnostic/therapeutic applications.
• Any biological behavior arises from the oligonucleotide produced after proper synthesis and deprotection, not from the protected amidite itself.

Buffer Applications

Not typically applicable. DMT-dG(dmf) Phosphoramidite is a moisture-sensitive organic reagent used in anhydrous, non-aqueous conditions for solid-phase DNA synthesis. It is not used to prepare aqueous buffers. For relevant guidance, see Solvent Selection, Reaction & Applications, and Reaction Conditions.

Green Alternatives

Sustainability considerations in oligonucleotide synthesis often focus on solvent and reagent selection rather than replacing the amidite itself.

Potential greener choices (literature/general):

• Solvents:
  • Replace dichloromethane (DCM) during detritylation with less hazardous alternatives (e.g., toluene or MeCN-rich blends) when instrument chemistry allows; verify detritylation efficiency and resin compatibility first.
  • Optimize acetonitrile usage by implementing low-dead-volume lines, on-demand delivery, and solvent recycling systems validated for water content.
• Activators and oxidants:
  • Use more benign activators such as ETT in MeCN and avoid high-toxicity acids/bases where possible.
  • Replace iodine oxidations with alternative oxidants only when validated to maintain coupling yields and sequence fidelity.

Comparison overview (general):

• DCM vs toluene/MeCN: DCM offers fast detritylation and good trityl solubility but has higher environmental/health concerns; toluene/MeCN reduces chlorinated waste but may require longer exposure or modified acid strengths.
• Solvent minimization: Process intensification and shorter cycle times lower overall solvent consumption without altering chemistry.

Trade-offs:

• Alternative solvents can change cycle kinetics, trityl colorimetry, and resin swelling—method revalidation is essential.

Note: There is no direct “green” substitute for DMT-dG(dmf) Phosphoramidite itself; improvements are achieved via process and solvent optimizations.

Pharmaceutical Uses

No therapeutic or clinical claims are made. In a manufacturing/formulation context (general):

• Role: A protected 2′-deoxyguanosine building block used to assemble DNA oligonucleotides that may become components of research-grade or, after appropriate process validation and GMP sourcing, development-stage oligonucleotide drug candidates.
• Process considerations: Selection of amidite grade, control of water content, and validation of deprotection/cleavage protocols are critical for impurity profiles (e.g., n–1 sequences, depurination products) and final oligo quality attributes.
• Regulatory status: Any use in GMP settings requires supplier qualification, defined specifications, and change control; pharmacopeial monographs generally do not exist for protected phosphoramidites, so in-house or supplier COA/SOPs govern quality.
• Residuals: Post-synthesis purification (e.g., RP-HPLC, cartridge desalting) removes protecting group remnants and process chemicals in the final oligonucleotide; validation of removal is mandatory for clinical materials.

Item-specific pharmacopeial or GMP statements: Not specified for this item; refer to CoA/Spec Sheet and consult your quality unit for suitability in regulated workflows.

Physical Properties

Item-specific numerical specifications are not provided. Consult the CoA/Spec Sheet for definitive values.

General/literature information for nucleoside phosphoramidites (for context only):

• Physical state: Often a foam, glassy solid, or low-melting solid; some appear as viscous oils depending on substitution and residual solvent.
• Color: Off-white to pale yellow is common for DMT-protected amidites due to the trityl chromophore.
• Solubility (literature/general): Freely soluble in anhydrous acetonitrile (MeCN); also soluble in dry dichloromethane (DCM), tetrahydrofuran (THF), and toluene mixtures used in synthesis platforms.
• Moisture sensitivity: High. Phosphoramidites hydrolyze with water to the corresponding phosphate/diol; strict anhydrous handling is required.
• Thermal behavior: Prolonged heating accelerates decomposition/oxidation of P(III). Avoid elevated temperatures except brief, controlled warming under dry inert gas to dissolve.
• UV absorbance: DMT and guanine absorb in the UV; DMT cation release at ~498 nm is commonly monitored during detritylation in oligo synthesis (instrument-dependent). This is an operational indicator, not a specification.

Do not treat the above as product specifications. For boiling/melting points, density, refractive index, water content, or UV cutoff: Not specified for this item; refer to CoA/Spec Sheet.

Quality and Grades

• Item grade: Moligand™ (manufacturer designation).
• Interpretation: Moligand™ typically denotes synthesis-grade building blocks designed for high-efficiency, automated solid-phase oligonucleotide assembly. Emphasis is generally placed on low moisture content, high coupling efficiency, and tight control of organic impurities and residual solvents.
• Item-specific specifications (e.g., assay/purity %, water content, residual activator, metal limits, UV profile): Not specified for this item; refer to CoA/Spec Sheet.

What grade means in practice (general for phosphoramidites):

• High coupling performance on DNA synthesizers across a range of activators (e.g., ETT, DCI, tetrazoles) and cycle times.
• Compatibility with standard capping and oxidation/sulfurization steps.
• Optimized protecting group set (DMT/dmf) for efficient deprotection and minimal side reactions under standard protocols.

Verification and QC recommendations:

• Inspect solution color/clarity in dry MeCN; excessive color or particulates can indicate hydrolysis or contamination.
• Check instrument detritylation trityl monitor traces for clean, high-intensity DMT release peaks early in a synthesis run.
• For critical applications, perform a short test synthesis (e.g., 10-mer) and analyze by LC–MS/HPLC to confirm coupling efficiency and deprotection performance.

Note: Always rely on the product’s CoA/SDS for definitive specifications and acceptance criteria.

Reaction and Applications

Primary application: Stepwise, solid-phase DNA synthesis (phosphoramidite method).

Key steps and how this amidite participates (literature/practice):

• Deprotection of 5′-DMT on the support-bound nucleoside using dilute acid (e.g., 3% TCA in DCM) to expose the 5′-OH.
• Activation and coupling: The 3′-phosphoramidite of DMT-dG(dmf) is activated by a tetrazole-type activator (e.g., ETT, DCI, 1H-tetrazole), generating a reactive phosphoramidite–tetrazolide which couples to the free 5′-OH on solid support to form a phosphite triester.
• Capping: Unreacted 5′-OHs are acetylated (Cap A/B) to suppress deletion sequences.
• Oxidation or sulfurization: Convert P(III) to P(V) phosphate or phosphorothioate using iodine/water/pyridine or sulfurizing reagents (e.g., PADS, DDTT).
• Repeat cycles to desired length; final detritylation yields the free 5′-OH (if required) before cleavage and base deprotection.

Why dmf protection for G:

• The dimethylformamidine group moderates guanine basicity and reduces depurination and side reactions during acid detritylation, improving sequence integrity.

Practical tips:

• Use rigorously dry MeCN and freshly prepared activator solutions.
• Maintain inert headspace in reagent bottles; backfill with argon/nitrogen after each access.
• Monitor DMT cation release to diagnose coupling efficiency and resin health in real time.

Other applications: Incorporation of guanine residues in modified oligonucleotides, handles for subsequent post-synthetic modifications at neighboring positions.

Reaction Conditions

General literature guidance for solid-phase DNA synthesis using DMT-dG(dmf) Phosphoramidite (verify on your platform):

• Solution preparation: Dissolve amidite at 0.05–0.1 M in anhydrous MeCN under inert gas. Gentle warming (≤35 °C) under dry conditions can assist dissolution.
• Activation: Use 0.25–0.5 M activator solutions in dry MeCN (e.g., ETT, DCI, or 1H-tetrazole). Typical coupling times range from 1–10 minutes depending on instrument and sequence.
• Detritylation: 2–3% TCA in DCM (or instrument-approved alternatives) for seconds to minutes; monitor trityl color/UV at ~498 nm to confirm completeness.
• Oxidation: Iodine (e.g., 0.02–0.05 M I2 in THF/MeCN/H2O/pyridine) for ~30–90 seconds; for phosphorothioates, use sulfurizing reagents (e.g., DDTT, PADS) per vendor guidance.
• Capping: Cap A (acetic anhydride in THF) and Cap B (NMI/DMAP in THF/pyridine) to block unreacted 5′-OHs.
• Cleavage and deprotection (post-synthesis): Concentrated ammonium hydroxide or AMA (ammonium hydroxide/methylamine) at ambient to elevated temperatures removes base protections (including dmf) and cleaves from support; exact times/temperatures depend on support/linker and any sequence modifications.
• Atmosphere: Maintain anhydrous, inert conditions for amidite and activator delivery lines.

Expected outcomes (typical): High coupling efficiencies (>98% per step in optimized systems) with clean DMT release profiles. Validate and optimize on your synthesizer. Item-specific recommended conditions: Not specified for this item; refer to CoA/Spec Sheet.

Safety and Handling

GHS classification, pictograms, and H-statements: Not specified for this item; refer to the SDS for authoritative safety information.

General safety guidance for phosphoramidites (literature/practice):

• Hazards: Moisture-sensitive P(III) species; may cause skin/eye irritation. Hydrolysis can generate amines and acidic/byproduct species. DCM, MeCN, and activators used alongside are flammable/toxic—assess combined risks.
• PPE: Laboratory coat, safety glasses or face shield, and appropriate chemically resistant gloves (e.g., nitrile). Use in a certified chemical fume hood.
• Handling: Work under dry, inert atmosphere (argon or nitrogen). Use anhydrous solvents and oven-dried/glovebox-dried glassware. Minimize headspace exposure; promptly recap vials with septa and backfill with inert gas.
• Incompatibilities: Water, alcohols, protic acids/bases (cause rapid hydrolysis). Strong oxidizers can convert P(III) to P(V) species. Avoid silica containing residual moisture without proper precautions.
• First aid (overview; defer to SDS): Inhalation—move to fresh air; seek medical attention if symptoms persist. Skin/eye contact—rinse with water for 15 minutes; remove contaminated clothing; obtain medical advice. Ingestion—rinse mouth; do not induce vomiting; seek medical attention.
• Waste: Collect amidite-containing solutions and activators as hazardous organic waste; segregate from oxidizers/reductants per institutional policy.
• Fire: Surrounding solvents dictate fire risk; use CO2, dry chemical, or foam as appropriate. Avoid water streams that could hydrolyze reactive contents.

Solvent Selection

This reagent is formulated for use in anhydrous organic solvents, primarily for automated oligonucleotide synthesis.

• Primary solvent (literature/practice):
  • Anhydrous acetonitrile (MeCN) is the standard solvent for dissolution, delivery, and coupling of phosphoramidites due to suitable polarity, low viscosity, and activator compatibility.
• Alternative/co-solvents (instrument- and method-dependent):
  • Dry dichloromethane (DCM) or DCM/MeCN mixtures can improve solubility for highly lipophilic DMT-protected amidites.
  • Toluene/MeCN and THF/MeCN blends are sometimes used to tune viscosity and delivery characteristics in certain synthesizers.
• Dielectric and polarity (general): MeCN is a polar aprotic solvent (dielectric constant ~37 at 20 °C, literature) that stabilizes tetrazolide intermediates and supports high coupling rates.
• Miscibility: MeCN is miscible with DCM, THF, and toluene; avoid protic solvents (water, alcohols) which cause hydrolysis.

When to choose alternatives:

• Poor solubility or slow syringe delivery: Add 10–30% DCM to MeCN, maintaining strict dryness.
• Moisture mitigation: Use freshly opened anhydrous solvent bottles or solvent dispensed from a solvent purification system into a glovebox.
• Instrument compatibility: Follow the synthesizer manufacturer’s validated solvent list and viscosity limits to prevent line occlusion or metering errors.

Note: Final solvent choice should be validated on your specific synthesis platform. Item-specific solvent restrictions: Not specified for this item; refer to CoA/Spec Sheet.

Storage and Reconstitution

Item-specific storage and shipping:

• Storage conditions: Protected from light, Store at -80°C.
• Shipped in: Dry ice packs + Cold packs.

General handling/reconstitution guidance (literature/practice):

• Upon receipt, keep frozen and protected from light. Warm to room temperature in a desiccator before opening to prevent moisture condensation.
• Open only under dry, inert atmosphere (glovebox or dry N2/Ar purge). Reseal promptly and backfill with inert gas.
• Reconstitution: Prepare solutions in anhydrous acetonitrile (commonly 0.05–0.1 M). If needed, use dry DCM/MeCN blends to improve solubility. Mix gently; brief warming (≤35 °C) under inert gas can aid dissolution.
• Aliquoting: Divide into single-use portions to minimize freeze–thaw and moisture exposure. Store aliquots in crimped/septum vials or screw-cap vials with PTFE liners under inert gas.
• Stability notes: Phosphoramidites are moisture- and oxygen-sensitive; limit time at ambient temperature. Discard solutions showing significant hydrolysis (e.g., poor coupling performance, abnormal trityl monitoring, or precipitates).

Any item-specific shelf-life, water content, stabilizers, or inhibitor details: Not specified for this item; refer to CoA/Spec Sheet.

Research use only: Yes (as stated).

Structure and Identity

DMT-dG(dmf) Phosphoramidite is a protected 2′-deoxyguanosine building block for automated DNA synthesis.

• SKU: D1496683
• Product name: DMT-dG(dmf) Phosphoramidite
• CAS: 330628-04-1
• PubChem CID: 136334904
• Grade: Moligand™
• Molecular formula: Not specified for this item; refer to CoA/Spec Sheet.
• Molecular weight: Not specified for this item; refer to CoA/Spec Sheet.
• SMILES: Not specified for this item; refer to CoA/Spec Sheet.
• InChIKey: Not specified for this item; refer to CoA/Spec Sheet.

Structural features (general/literature description):

• Core nucleoside: 2′-deoxyguanosine (purine base linked to 2-deoxyribose via β-N9-glycosidic bond).
• Base protection: Exocyclic N2 of guanine protected as dimethylformamidine, often abbreviated “dmf” or “dmf-protected G,” to moderate guanine basicity and reduce side reactions during synthesis.
• 5′-O protection: 4,4′-dimethoxytrityl (DMT) ether to enable acid-labile, stepwise detritylation during solid-phase synthesis.
• 3′-Phosphoramidite: Typically 3′-O-(2-cyanoethyl N,N-diisopropyl)phosphoramidite, enabling tetrazole-activated coupling to a growing oligonucleotide on solid support.
• Stereochemistry: Multiple stereocenters in the 2-deoxyribose (natural D-configuration). The P(III) center is prochiral and forms a transient linkage during coupling/oxidation on solid phase.

2D description in words (general): A purine (guanine) ring bearing a dmf substituent on N2, attached at N9 to a 2-deoxyribose whose 5′-OH is capped by a DMT group, and 3′-O is functionalized as a 2-cyanoethyl N,N-diisopropyl phosphoramidite.

Synthetic Utility

DMT-dG(dmf) Phosphoramidite is a key monomer in phosphoramidite chemistry for DNA assembly.

Functional group strategy (general):

• 5′-O-DMT: Provides an acid-labile temporary protection enabling iterative chain growth with spectrophotometric monitoring via trityl cation release.
• N2-dmf on guanine: Stabilizes guanine during acid treatment, suppressing depurination and O6-related side reactions; removable under standard ammonolysis.
• 3′-O-phosphoramidite (2-cyanoethyl N,N-diisopropyl): Highly reactive toward 5′-OH under tetrazole activation; converts to stable phosphate after oxidation.

Retrosynthetic and forward utility:

• Enables the installation of G at any position with compatibility across standard DNA protecting group sets (e.g., dA(Bz), dC(Ac or iBu), dT).
• Compatible with numerous solid supports (CPG, polystyrene) and linkers (Universal, succinylated) for synthesis of oligos from short primers to long sequences.
• Supports downstream chemistries: Once incorporated, adjacent positions can be modified (e.g., post-synthetic labeling) without perturbing the G base functionality after deprotection.

Integration with named methodologies:

• Beaucage/Caruthers phosphoramidite method (solid-phase).
• Oxidation with I2/H2O or sulfurization (e.g., DDTT) for phosphorothioates.

This reagent’s protection pattern and reactivity are optimized for robust, high-fidelity DNA assembly under standard synthesis cycles.

Target Specificity

Not applicable. This product is a chemical building block for oligonucleotide synthesis and does not possess biological target specificity on its own. Any sequence-specific interactions arise from the finalized oligonucleotide constructed using this amidite.