5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
[CAS 98796-51-1]

Identification

• Classification: Organic raw materials >> Amino compound >> Amide compound
• Name: 5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
• Synonyms: 5'-O-[Bis(4-methoxyphenyl)phenylmethyl]-thymidine 3'-[2-cyanoethyl bis(1-methylethyl)phosphoramidite]
• Molecular Formula: C₄₀H₄₉N₄O₈P
• Molecular Weight: 744.81
• CAS Registry Number: 98796-51-1
• EC Number: 685-410-3
• SMILES: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COC(C3=CC=CC=C3)(C4=CC=C(C=C4)OC)C5=CC=C(C=C5)OC)OP(N(C(C)C)C(C)C)OCCC#N

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

chemBlink Chemical Story

5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is a protected nucleoside phosphoramidite used as a specialized building block in the chemical synthesis of modified DNA oligonucleotides. It belongs to the class of phosphoramidite reagents developed for automated solid-phase oligonucleotide synthesis. The compound is derived from 3'-deoxythymidine and contains protecting groups that allow selective chemical reactions during DNA strand assembly.

The development of nucleoside phosphoramidite chemistry was a major advancement in synthetic nucleic acid chemistry. Earlier methods for oligonucleotide preparation required multiple purification steps and had limited efficiency for longer sequences. The phosphoramidite approach introduced a practical method for automated DNA synthesis by enabling repeated cycles of nucleotide addition with controlled protection and deprotection of reactive functional groups.

The compound is based on 3'-deoxythymidine, a thymidine analogue lacking the hydroxyl group normally present at the 3' position of natural thymidine. Thymidine is one of the four nucleosides found in DNA, where it participates in base pairing with adenosine. Modified thymidine derivatives such as 3'-deoxythymidine have been used in nucleic acid chemistry to investigate DNA structure, synthesis, and function.

The molecule contains a thymine nucleobase attached to a deoxyribose-derived sugar framework. The thymine base contains carbonyl and nitrogen functionalities that participate in hydrogen bonding in natural DNA. During chemical synthesis, nucleobase functional groups must be controlled to prevent unwanted side reactions, allowing selective formation of the desired oligonucleotide sequence.

The 5'-hydroxyl group of the sugar is protected with a dimethoxytrityl group. The 4,4'-dimethoxytrityl protecting group is widely used in oligonucleotide synthesis because it can be removed selectively under acidic conditions. Removal of this group exposes the 5'-hydroxyl position, enabling the next nucleotide coupling step in an automated synthesis cycle.

The phosphoramidite functionality is attached at the 2' position of the sugar. This phosphorus-containing group provides the reactive site required for nucleotide coupling reactions. In automated oligonucleotide synthesis, the phosphoramidite reacts with a free hydroxyl group on a growing oligonucleotide chain after activation by a suitable reagent, forming a new phosphorus-containing linkage.

The phosphoramidite group contains a 2-cyanoethyl protecting group and an N,N-diisopropylamino group. The 2-cyanoethyl group protects the phosphorus center during synthesis and can be removed during the final deprotection process. The diisopropylamino group functions as a leaving group during coupling reactions, allowing formation of the internucleotide bond.

The compound is primarily used in the preparation of modified oligonucleotides. Because it is derived from 3'-deoxythymidine rather than standard thymidine, incorporation of this building block introduces a specific structural modification into synthetic DNA molecules. Such modified oligonucleotides are valuable tools in studies of nucleic acid chemistry and molecular biology.

Synthetic DNA containing modified nucleoside units is used in many research applications, including investigations of DNA structure, enzyme interactions, molecular recognition, and nucleic acid-based technologies. Phosphoramidite reagents with specialized sugar modifications allow researchers to systematically alter oligonucleotide properties.

The chemical properties of this compound are determined by the combination of the nucleoside structure, aromatic dimethoxytrityl protecting group, and reactive phosphoramidite moiety. The protecting groups provide controlled chemical behavior during synthesis, while the nucleoside component determines the structural features introduced into the final oligonucleotide.

Because phosphoramidites are sensitive to moisture and oxidation, they are generally handled under carefully controlled conditions during synthesis. Their stability and reactivity are optimized for use in automated DNA synthesizers.

Overall, 5'-Dimethoxytrityl-3'-deoxythymidine 2'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite is a specialized protected thymidine analogue used in synthetic oligonucleotide chemistry. Its carefully designed protecting groups and modified nucleoside structure make it a valuable reagent for producing DNA molecules with defined structural modifications for research applications.

References

2009. Sulfurization with Lawesson's Reagent. Science of Synthesis.
URL: https://science-of-synthesis.thieme.com/app/text/?id=SD-042-01049