102212-98-6

Basic information

• Product Name: 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite
• Synonyms: REF DUPL: DMT-dC(bz) Phosphoramidite;Bz-dC Phosphoramidite;N4-Benzoyl-2'-deoxy-5'-O-DMT-cytidine 3'-CE phosphoramidite ,98%;N4-Benzoyl-2'-deoxy-5'-O-DMT-cytidine 3'-CE phosphoramidite;2'-DEOXYCYTIDINE PHOSPHORAMIDITE;N4-Benzoyl-2'-deoxy-5'-O-DMT-cytidine 3'-CE phosphoraMidite;N4-Benzoyl-5′-O-(4,4′-dimethoxytrityl)-2′-deoxycytidine-3′-O-[O-(2-cyanoethyl)-N,N′-diisopropylphosphoramidite];N6-Benzoyl-5'-O-DMT-2'-deoxycytidine-3'-CE Phosphoramidite
• CAS NO: 102212-98-6
• Molecular Formula: C₄₆H₅₂N₅O₈P
• Molecular Weight: 833.91
• EINECS: 2017-001-1
• Mol File: 102212-98-6.mol
• Article Data: 11

Chemical Properties

• Appearance: white to off-white/
• Density: 1.23 at 20℃
• Vapor Pressure: 0-0Pa at 20-50℃
• Storage Temp.: Store at -20°C
• Solubility: Chloroform, DMSO, Methanol (Slightly)
• PKA: 8.65±0.20(Predicted)
• CAS DataBase Reference: 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite(CAS DataBase Reference)
• NIST Chemistry Reference: 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite(102212-98-6)
• EPA Substance Registry System: 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite(102212-98-6)

Safety Data

• Safety Statements: 24/25
• WGK Germany: 3
• Hazardous Substances Data: 102212-98-6(Hazardous Substances Data)

Usage

Description

5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite, also known as 5'-O-DMT-N4-Benzoyl-2'-deoxycytidine 3'-CE phosphoramidite, is a chemical compound used in the synthesis of modified oligonucleotides. It is characterized by the presence of a 4,4'-dimethoxytrityl group at the 5'-O position, a benzoyl group at the N4 position, a 2'-deoxycytidine moiety, and a 3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite group. 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite plays a crucial role in the development of novel antisense oligonucleotides with unique structural features and potential therapeutic applications.

Uses

Used in Pharmaceutical Industry:
5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite is used as a key intermediate in the synthesis of antisense oligonucleotides for the development of new therapeutic agents. These modified oligonucleotides contain conformationally constrained methoxyaminomethylene, aminooxymethylene, and aminomethylene bridged nucleoside analogs, which can improve the stability, binding affinity, and biological activity of the resulting antisense molecules.
Used in Research and Development:
In the field of research and development, 5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite serves as a valuable tool for the design and synthesis of novel antisense oligonucleotides with unique structural features. These modified oligonucleotides can be used to study the mechanisms of gene regulation, develop new therapeutic strategies, and investigate the potential of antisense technology in various diseases and conditions.
Used in Diagnostic Applications:
5'-O-(4,4'-Dimethoxytrityl)-N4-benzoyl-2'-deoxycytidine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite can also be employed in the development of diagnostic tools and assays, such as DNA microarrays and biosensors, that rely on the specific recognition and binding of modified oligonucleotides to target nucleic acid sequences. The unique structural features of the modified antisense oligonucleotides synthesized using this compound can enhance the sensitivity, specificity, and reliability of these diagnostic applications.

Synthesis

These Examples illustrate the phosphitylation of several protected nucleoside reagents with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of several activators according to the present invention. Eleven phosphitylation reactions (1-11) comprising reacting a protected nucleoside reagent with 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite in the presence of an acid-base activator according to the present invention were conducted, and the product yields of each calculated, as described in the General Procedure, below. The various combinations of protected nucleoside, activator base, activator acid, solvent, and yield for each of the 11 reactions are listed in Table 1. General Procedure: The activator base (1.1 to 1.2 equivalents) is added to the solvent and 0.95 to 1.1 equivalents of activator acid is subsequently added thereto at ambient temperature to form the activator solution. About 1 equivalent of the protected nucleoside is dissolved in about 10 equivalents of the solvent in a separate vessel and about 3 equivalents of the solvent is then distilled off under reduced pressure. About 1 to 1.2 equivalents of 2-Cyanoethyl-N,N,N',N'-tetraisopropylphosphordiamidite is added to the nucleoside mixture at ambient temperature, and the activator solution prepared previously is then added to the nucleoside mixture at ambient temperature with vigorous stirring. After 12 hours, the reaction mixture is diluted with toluene and washed with water. The organic layer is separated, dried over sodium sulfate if necessary, and concentrated under reduced pressure. The yield of the desired amidite is then calculated using HPLC techniques, that is, the resulting product mixture is run through an HPLC column using an appropriate eluent, and the area under the HPLC peaks used to determine the %yield of product in the mixture.

Upstream product

• 102691-36-1 N,N,N',N'-tetraisopropyl 2-cyanoethylphosphorodiamidite 
• 67219-55-0 4-N-Benzoyl-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)cytidine 
• 174647-46-2 2-cyanoethoxy(N,N-diisopropylamino)3-nitro-1,2,4-triazolylphosphine 
• 140613-57-6 5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine-3'-O-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite] 
• 98-88-4 benzoyl chloride 
• 93-97-0 benzoic acid anhydride 
• 124482-92-4 2-cyanoethyl-N,N-(diisopropylamino)chlorophosphine 
• 133728-83-3 C₄₉H₆₂N₅O₇P 
• 109-78-4 3-Hydroxypropionitrile 
• 108-18-9 diisopropylamine 
• 40615-36-9 4,4'-dimethoxytrityl chloride 
• 7087-68-5 N-ethyl-N,N-diisopropylamine 
• 4836-13-9 N₄-benzoyl-2'-deoxycytidine 
• 951-77-9 2'-Deoxycytidine 

Downstream Products

• 118380-93-1 Phosphoric acid (2R,3S,5R)-5-(4-amino-2-oxo-2H-pyrimidin-1-yl)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-tetrahydro-furan-3-yl ester (2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethyl ester; compound with ammonia 
• 152998-05-5 N-benzoyl-5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-deoxy-cytidine 3'-(2-cyanoethylphosphonate) 
• 1055030-11-9 Phosphoric acid (2R,3S,5R)-5-(4-benzoylamino-2-oxo-2H-pyrimidin-1-yl)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-tetrahydro-furan-3-yl ester 2-cyano-ethyl ester (R)-2,2-dimethyl-[1,3]dioxolan-4-ylmethyl ester 
• 656249-30-8 5'-O-DMTr-dC^Bzps_CNEdG^i-Bu-3'-O-Lev 

Relevant articles and documents

A novel phosphitylating reagent for in situ generation of deoxyribonucleoside phosphoramidites

A new phosphitylating reagent, 2-cyanoethoxy(N,N-diisopropylamino)3-nitro-1,2,4-triazolylphosphine (1), has been prepared and effectively used in in situ generation of 5'-DMT-nucleoside phosphoramidites and automated syntheses of oligonucleotides.

Microwave-assisted preparation of nucleoside-phosphoramidites

Microwave-assisted phosphitylation of sterically hindered nucleosides is demonstrated to be an efficient method for the preparation of corresponding phosphoramidites (otherwise onerous under standard conditions) and is shown to be general in its applicability. the Partner Organisations 2014.

Overcoming hydrolytic sensitivity and low solubility of phosphitylation reagents by combining ionic liquids with mechanochemistry

Ionic liquids have been used in combination with ball milling on a range of chlorophosphoramidite reagents to phosphitylate nucleosides and 2-deoxynucleosides. The enhanced stability offered by the ionic liquid mediated processes combined with efficient mass transfer induced by ball milling has enabled excellent yields to be obtained even when using small dialkyl amino groups as well as the more commonly used diisopropylamino protection.