67219-55-0

Basic information

• Product Name: 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine
• Synonyms: DMT- Bz- dC;N4-Benzoyl-2'-deoxy-5'-O-DMT-a-cytidine;N4-Benzoyl-2'-deoxy-5'-O-DMT-cytidine;N4-Benzoyl-5'-O-(4,4'-diMethoxytrityl)-2'-deoxycytidine;N-Benzoyl-5'-O-(4,4'-diMethoxytrityl)-2'-deoxycytidine;N4-Bz-DMT-dC;n-benzoyl-5’-o-[bis(4-methoxyphenyl)phenylmethyl]-2’-deoxy-cytidin;N4-BENZOYL-5'-O-(4,4'-DIMETHOXYTRITYL)-2'-DEOXYCYTIDINE
• CAS NO: 67219-55-0
• Molecular Formula: C₃₇H₃₅N₃O₇
• Molecular Weight: 633.69
• EINECS: 266-605-9
• Product Categories: Biochemicals and Reagents;Building Blocks;C12 to C30+;Chemical Synthesis;Heterocyclic Building Blocks;Nucleoside Analogs;Nucleosides;Nucleotides;Oligonucleotides;Pyrimidines;Organics;Biochemistry;Nucleosides and their analogs;Nucleosides, Nucleotides & Related Reagents;Nucleic acids
• Mol File: 67219-55-0.mol

Chemical Properties

• Melting Point: 119 °C
• Boiling Point: 668.71°C (rough estimate)
• Appearance: Off-white powder
• Density: 1.2234 (rough estimate)
• Refractive Index: 58 ° (C=1, MeOH)
• Storage Temp.: −20°C
• PKA: 8.67±0.20(Predicted)
• Water Solubility: 100μg/L at 20℃
• BRN: 601627
• CAS DataBase Reference: 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine(CAS DataBase Reference)
• NIST Chemistry Reference: 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine(67219-55-0)
• EPA Substance Registry System: 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine(67219-55-0)

Safety Data

• Hazard Codes: Xn,Xi,T
• Statements: 40-36/37/38-20/21/22-46-45
• Safety Statements: 36/37-36-26-22-45-53
• RIDADR: UN 3077 9 / PGIII
• WGK Germany: 1
• F: 1-3-10
• Hazardous Substances Data: 67219-55-0(Hazardous Substances Data)

Usage

Uses

Used in Synthetic Modified DNA and RNA:
5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine is used as a reactant for the synthesis of modified DNA and RNA, specifically in the site-selective RNA activation by acridine-modified oligodeoxynucleotides in metal-ion catalyzed hydrolysis. This application allows for the development of targeted therapies and diagnostic tools in molecular biology.
Used in Research:
As a research tool, 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine is employed in anti-viral and anti-cancer studies. Its unique structure and properties make it a valuable compound for investigating the mechanisms of viral replication and cancer cell growth, potentially leading to the discovery of novel therapeutic agents.
Used in Diels-Alder Reactions:
The 3′-O-(2-cyanoethyl)-N,N-diisopropylphosphoramidite derivatives of 5'-O-Dimethoxytrityl-N-benzoyl-desoxycytidine (DMT-dCBz) are involved in Diels-Alder reactions between diene-modified oligonucleotides and maleimide-derivatized peptides. This application is crucial for the development of new chemical linkages and conjugation strategies in biochemistry and materials science.

Flammability and Explosibility

Notclassified

InChI:InChI=1/C37H35N3O7/c1-44-29-17-13-27(14-18-29)37(26-11-7-4-8-12-26,28-15-19-30(45-2)20-16-28)46-24-32-31(41)23-34(47-32)40-22-21-33(39-36(40)43)38-35(42)25-9-5-3-6-10-25/h3-22,31-32,34,41H,23-24H2,1-2H3,(H,38,39,42,43)

Upstream product

• 118352-74-2 5'-O-(4,4'-dimethoxytrityl)-4-N-benzoyl-2'-deoxycytidine-3'-H-phosphonate triethylammonium salt 
• 40615-36-9 4,4'-dimethoxytrityl chloride 
• 93-97-0 benzoic acid anhydride 
• 951-77-9 2'-Deoxycytidine 
• 116003-04-4 N₄-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine-3-O-[O-(2-cyanoethyl)-N,N-(diisopropyl)]phosphoramidite 
• 3992-42-5 2'-deoxycytidine monohydrochloride 
• 98-88-4 benzoyl chloride 
• 3019-98-5 pentachlorophenyl benzoate 
• 1548-84-1 pentafluorophenyl benzoate 
• 65-85-0 benzoic acid 
• 152998-05-5 N-benzoyl-5'-O-[bis(4-methoxyphenyl)phenylmethyl]-2'-deoxy-cytidine 3'-(2-cyanoethylphosphonate) 
• 4836-13-9 N₄-benzoyl-2'-deoxycytidine 
• 7396-95-4 2,4,5-Trichlorophenyl benzoate 
• 31501-22-1 N⁴-benzoyl-1-(3',5'-di-O-benzoyl-2'-deoxy-β-D-ribofuranosyl)-cytosine 

Downstream Products

• 74405-44-0 5'-O-dimethoxytrityl-N-benzoyldeoxycytidine 3'-succinate 
• 93134-40-8 N⁴-Benzoyl-5'-O-(dimethoxytrityl)-3'-O-(tert-butyldimethylsilyl)-2'-deoxycytidine 
• 93134-38-4 (2R,3S,5R)-5-(4-benzamido-2-oxopyrimidin-1(2H)-yl)-2-((bis(4-methoxyphenyl)(phenyl)methoxy)methyl)tetrahydrofuran-3-yl-4-oxopentanoate 
• 85532-80-5 C₄₈H₅₀N₅O₁₄P 
• 93134-55-5 C₅₂H₅₅N₈O₁₄P 
• 87007-45-2 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 (2R,3S,5R)-5-(6-benzoylamino-purin-9-yl)-3-hydroxy-tetrahydro-furan-2-ylmethyl ester methyl ester 
• 160971-60-8 C₃₈H₃₇ClN₃O₇P 
• 161000-52-8 (Rp,Sp)-N⁴-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxycytidine-3'-O-(N,N-diisopropylamino)-(2,2,2-trifluoroethyl)phosphoramidites 
• 162611-44-1 C₄₃H₄₈FN₄O₇P 
• 118352-74-2 5'-O-(4,4'-dimethoxytrityl)-4-N-benzoyl-2'-deoxycytidine-3'-H-phosphonate triethylammonium salt 
• 162611-36-1 Diisopropyl-phosphoramidous 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 4-nitro-phenyl ester 
• 90678-78-7 N-Bz-5'-O-DMT-dC 3'-H-phosphonate 
• 170935-19-0 N-{1-[(2R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-(3-methyl-[1,3,2]oxazaphospholidin-2-yloxy)-tetrahydro-furan-2-yl]-2-oxo-1,2-dihydro-pyrimidin-4-yl}-benzamide 
• 166758-07-2 4-N-benzoyl-2'-deoxy-3'-O-tert-butyldiphenylsilyl-5'-O-dimethoxytritylcytidine 

Relevant articles and documents

A new and convenient approach for the preparation of β-cyanoethyl protected trinucleotide phosphoramidites

Herein we report a convenient approach for the preparation of fully protected trinucleotide synthons to be used for the synthesis of gene libraries. The trinucleotide synthons bear β-cyanoethyl groups at the phosphate residues, and thus can be used in standard oligonucleotide synthesis without additional steps for deprotection and work-up.

Exploring the synthesis of masked phosphoramido 6-vinylcytidine derivatives as building blocks for cross-linking oligonucleotides

In the present work the synthesis of building blocks (2a,b), bearing a masked form of the reactive vinyl group bound to the C-6 position of a cytidine derivative, has been studied. The understanding of byproduct formation together with conformational considerations let us to plan a straightforward approach for the synthesis of the target compounds.

Metallic salt of N4-acylcytidine derivatives, and a method for producing N4-acylcytidine derivatives using the same

The present invention provides a method for producing a high purity N4-acylcytidine derivative. More specially, the invention provides a compound represented by the formula (1): wherein R1 represents a hydrogen atom, an alkyl group having 1 to 4 carbon atoms, an alkenyl group having 2 to 4 carbon atoms, an alkynyl group having 2 to 4 carbon atoms, a perfluoroalkyl group having 1 to 4 carbon atoms, or a halogen atom; R2 is a hydrogen atom, an alkoxyl group having 1 to 4 carbon atoms, an alkoxyl group having 1 to 4 carbon atoms with a substituent, or a halogen atom; R3 represents a methyl group or a phenyl group; and M represents a positive ion of an alkali metal or an alkaline earth metal, and a compound represented by the formula (2): wherein R1, R2, and R3 are as defined above, produced by using the compound represented by the formula (1).

Nucleosidyl-O-methylphosphonates: A pool of monomers for modified oligonucleotides

An unique set of 5′-O- and 3′-O-phosphonomethyl derivatives of four natural 2′-deoxyribonucleosides, 1-(2-deoxy-β-D-threo- pentofuranosyl)thymine, 5′-O- and 2′-O-phosphonomethyl derivatives of 1-(3-deoxy-β-D-erythro-pentofuranosyl)thymine, and 1-(3-deoxy-β-D- threo-pentofuranosyl)thymine has been synthesized as a pool of monomers for the synthesis of modified oligonucleotides. The phosphonate moiety was protected with 4-methoxy-1-oxido-2-pyridylmethyl ester group, serving also as an intramolecular catalyst in the coupling step.

Method for purifying protected 2'-deoxycytidines and hydrated crystals thereof

A protected 2′-deoxycytidine is purified by precipitating the protected 2′-deoxycytidine represented by general formula (3) in the form of a hydrated crystal from a solution containing the protected 2′-deoxycytidine and water, and by recovering the protected 2′-deoxycytidine: wherein R1 represents a 4-methoxytrityl, 4,4′-dimethoxytrityl, or triphenylmethyl group; and B1 represents a cytosine group having a protected amino group. The compound represented by general formula (3) is, in particular, a protected 2′-deoxycytidine represented by formula (4): The 2′-deoxycytidine is used as a raw material for antisense DNA.

Nucleoside recovery in DNA and RNA synthesis

Nucleoside phosphoramidites and H-phosphonate diesters can be converted to nucleosides under mild conditions and in high yields by reaction with polyhydroxy alcohols.

Dephosphonylation of protected deoxynucleoside and oligodeoxynucleotide H-phosphonates

The conversion of four 5'-O-(4,4'-dimethoxytrityl)-2'- deoxyribonucleoside 3'-H-phosphonates 1 (B=4, 5, 6 and 7) into their partially-protected nucleoside precursors 3 (B=4, 5, 6 and 7, respectively) in good isolated yields is described. The procedure used is also suitable for the dephosphonylation of protected oligonucleotide H-phosphonate blocks.

A mild and efficient method for the preparation of 5'-dimethoxytrityl- 2'-deoxynucleoside using poly(4-vinylpyridine)costyrene

5'-O-4,4'-Dimethoxytrityl-2'-deoxynucleosides have been synthesized in high yield by the reaction of 2'-deoxynucleosides with 4, 4'-dimethoxytrityl chloride in acetonitrile using poly (4-vinylpyridine)-costyrene(styrene 10%).

Nucleosides and nucleotides. 185. Synthesis and biological activities of 4'α-C-branched-chain sugar pyrimidine nucleosides

A series of 4'α-C-branched-chain pyrimidine nucleosides was synthesized from 2'-deoxycytidine or uridine. In the 2'-deoxycytidine series, the substituent at the 4'α-position affected cytotoxicity against L1210 mouse leukemic cells in vitro in the order Me (23) > CN (22)> C≡CH (21) > CH=CH2 (19) > Et (24) > CH=CHCl (20). However, uridine and cytidine derivatives with ethynyl and cyano groups at the 4'α-position did not show any cytotoxicity. The antiviral activities of these nucleosides against HSV-1, HSV-2, and HIV- 1 in vitro were also examined. Compounds 22 and 23 showed antiviral activities against HSV-1 and HSV-2 without showing significant toxicity to the host cells (MRC-5 cells). Although almost all of the nucleosides showed anti-HIV-1 activities, they were also cytotoxic to the host cells (MT-4).

Synthesis and characterization of phosphate-modified DNA-dimers with fluorine as an uncharged ligand

The potential of the dinucleosidylphosphorofluoridates dCpFdG and dApFdT is described. Side products of the phosphoramidite coupling reaction are synthesized and characterized by 31P-NM]R-spectroscopy.