5'-O-(4,4'-Dimethoxytrityl)-N6-benzoyl-2'-deoxyadenosine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite
[CAS 98796-53-3]

Identification

• Classification: Biochemical >> Nucleoside drugs >> Nucleoside intermediate
• Name: 5'-O-(4,4'-Dimethoxytrityl)-N6-benzoyl-2'-deoxyadenosine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite
• Synonyms: N-Benzoyl-5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-deoxy-adenosine 3'-[2-cyanoethyl bis(1-methylethyl)phosphoramidite]
• Molecular Formula: C₄₇H₅₂N₇O₇P
• Molecular Weight: 857.93
• CAS Registry Number: 98796-53-3
• EC Number: 685-521-7
• SMILES: CC(C)N(C(C)C)P(OCCC#N)O[C@H]1C[C@@H](O[C@@H]1COC(C2=CC=CC=C2)(C3=CC=C(C=C3)OC)C4=CC=C(C=C4)OC)N5C=NC6=C(N=CN=C65)NC(=O)C7=CC=CC=C7

Safety Data

• Hazard Symbols: GHS07 Warning
• Risk Statements: H319
• Safety Statements: P264+P265-P280-P305+P351+P338-P337+P317

Hazard Classification

Hazard	Class	Category Code	Hazard Statement
Eye irritation	Eye Irrit.	2	H319
Acute toxicity	Acute Tox.	4	H302

Discovery and Applications

5'-O-(4,4'-Dimethoxytrityl)-N6-benzoyl-2'-deoxyadenosine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite is a protected adenosine phosphoramidite used as a nucleotide building block in the chemical synthesis of DNA oligonucleotides. It belongs to the class of nucleoside phosphoramidites developed for automated solid-phase DNA synthesis. The compound contains a protected 2'-deoxyadenosine unit and a phosphoramidite group that enables controlled incorporation of adenine residues into synthetic DNA sequences.

The development of phosphoramidite-based oligonucleotide synthesis was a major advance in nucleic acid chemistry. Traditional methods for assembling DNA fragments were limited by reaction efficiency and required complex procedures. The phosphoramidite approach introduced an automated method in which protected nucleosides are added stepwise to a growing oligonucleotide chain. This technology enabled the routine preparation of synthetic DNA molecules for molecular biology and biotechnology applications.

The compound is derived from 2'-deoxyadenosine, one of the four naturally occurring nucleosides present in DNA. In natural DNA, adenine forms a complementary base pair with thymine through hydrogen bonding interactions. During chemical synthesis, reactive groups on adenine and the sugar moiety must be selectively protected to ensure efficient and accurate nucleotide coupling.

The adenine nucleobase contains an exocyclic amino group at the N6 position. In this compound, the N6-amino group is protected with a benzoyl group. The benzoyl protecting group reduces the reactivity of the amino functionality during oligonucleotide synthesis and prevents unwanted side reactions. After the desired DNA sequence has been assembled, the protecting group can be removed during the final deprotection process to restore the natural adenine structure.

The 5'-hydroxyl group of the deoxyribose sugar is protected with a 4,4'-dimethoxytrityl group. This protecting group is widely used in nucleoside chemistry because it can be selectively removed under mild acidic conditions. During automated DNA synthesis, removal of the dimethoxytrityl group exposes the 5'-hydroxyl group, allowing the next nucleotide to be added in the sequence.

The 3'-position of the sugar is converted into a phosphoramidite functionality. This phosphorus-containing group is responsible for the coupling reaction that forms the DNA backbone. When activated by a suitable reagent, the phosphoramidite reacts with a free hydroxyl group on the growing oligonucleotide chain, producing a new phosphorus-containing linkage.

The phosphoramidite moiety contains a 2-cyanoethyl protecting group and an N,N-diisopropylamino group. The 2-cyanoethyl group protects the phosphorus center during repeated synthesis cycles and is removed during the final processing of the oligonucleotide. The diisopropylamino group serves as a leaving group during the coupling reaction, allowing formation of the internucleotide bond.

The primary application of this compound is the preparation of synthetic DNA molecules containing adenine residues. It is used in automated oligonucleotide synthesizers to construct DNA sequences required for molecular biology research, genetic analysis, sequencing, and biotechnology applications.

Synthetic oligonucleotides produced from protected adenosine phosphoramidites are used as primers, probes, and research reagents. They are essential tools in techniques that require precisely defined DNA sequences, including amplification methods, hybridization studies, and investigations of nucleic acid structure and function.

The chemical design of this phosphoramidite reagent illustrates the importance of protecting group strategies in nucleic acid synthesis. The dimethoxytrityl group controls reactivity at the 5'-position, the benzoyl group protects the adenine amino functionality, and the phosphoramidite group provides the reactive site required for chain extension.

The physical and chemical properties of the compound are determined by its combination of aromatic protecting groups, nucleoside structure, and phosphorus-containing functionality. The molecule contains multiple oxygen and nitrogen atoms that contribute to polarity, while the aromatic dimethoxytrityl and benzoyl groups provide hydrophobic character. Due to the moisture sensitivity of phosphoramidites, these compounds are typically handled under dry conditions.

Overall, 5'-O-(4,4'-dimethoxytrityl)-N6-benzoyl-2'-deoxyadenosine-3'-(2-cyanoethyl-N,N-diisopropyl)phosphoramidite is an essential protected nucleoside reagent for DNA synthesis. Its selective protecting groups and reactive phosphoramidite functionality enable efficient and controlled construction of synthetic oligonucleotides used throughout molecular biology and biotechnology research.