19083-35-3

Basic information

• Product Name: 5-[(benzyloxy)methyl]-1-(2-deoxypentofuranosyl)pyrimidine-2,4(1H,3H)-dione
• Synonyms: 5-Benzyloxymethyl-1-(4-hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-1H-pyrimidine-2,4-dione
• CAS NO: 19083-35-3
• Molecular Formula: C₁₇H₂₀N₂O₆
• Molecular Weight: 348.3505
• Mol File: 19083-35-3.mol
• Article Data: 4

Chemical Properties

• Density: 1.385g/cm³
• Refractive Index: 1.605
• CAS DataBase Reference: 5-[(benzyloxy)methyl]-1-(2-deoxypentofuranosyl)pyrimidine-2,4(1H,3H)-dione(CAS DataBase Reference)
• NIST Chemistry Reference: 5-[(benzyloxy)methyl]-1-(2-deoxypentofuranosyl)pyrimidine-2,4(1H,3H)-dione(19083-35-3)
• EPA Substance Registry System: 5-[(benzyloxy)methyl]-1-(2-deoxypentofuranosyl)pyrimidine-2,4(1H,3H)-dione(19083-35-3)

Safety Data

• Hazardous Substances Data: 19083-35-3(Hazardous Substances Data)

Upstream product

• 1028383-90-5 N³-tert-butyloxycarbonyl-5-bromomethyl-3',5'-bis-O-tert-butyldimethylsilyl-2'-deoxyuridine 
• 100-51-6 benzyl alcohol 
• 13035-61-5 1,2,3,5-tetraacetylribose 
• 304849-80-7 5-[(benzyloxy)methyl]-3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)uridine 
• 98808-20-9 O,O'-bis(trimethylsilyl)-5-benzyloxymethyluracil 
• 4330-34-1 methyl 3,5-di-O-toluoyl-2-deoxy-D-ribofuranose 
• 7226-75-7 5-benzyloxymethyl-3',5'-di-O-toluoyl-2'-deoxyuridine 
• 304849-81-8 5-[(benzyloxy)methyl]-2'-deoxy-3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)uridine 
• 7295-02-5 benzyl hydroxymethyl uridine 
• 13111-67-6 2',3',5'-tri-O-acetyl-5-[(benzyloxy)methyl]uridine 
• 24751-66-4 5-[(benzyloxy)methyl]uridine 

Downstream Products

• 304849-87-4 5-benzyloxymethyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 3'-(N,N-diisopropyl)-2-cyanoethyl phosphoramidite 
• 304849-85-2 5-[(benzyloxy)methyl]-2'-deoxy-5'-O-(4,4'-dimethoxytrityl)uridine 
• 50-89-5 thymidine 

Relevant articles and documents

Base-modified thymidines capable of terminating DNA synthesis are novel bioactive compounds with activity in cancer cells

Current FDA-approved chemotherapeutic antimetabolites elicit severe side effects that warrant their improvement; therefore, we designed compounds with mechanisms of action focusing on inhibiting DNA replication rather than targeting multiple pathways. We previously discovered that 5-(α-substituted-2-nitrobenzyloxy)methyluridine-5′-triphosphates were exquisite DNA synthesis terminators; therefore, we synthesized a library of 35 thymidine analogs and evaluated their activity using an MTT cell viability assay of MCF7 breast cancer cells chosen for their vulnerability to these nucleoside derivatives. Compound 3a, having an α-tert-butyl-2-nitro-4-(phenyl)alkynylbenzyloxy group, showed an IC50 of 9 ± 1 μM. The compound is more selective for cancer cells than for fibroblast cells compared with 5-fluorouracil. Treatment of MCF7 cells with 3a elicits the DNA damage response as indicated by phosphorylation of γ-H2A. A primer extension assay of the 5′-triphosphate of 3a revealed that 3aTP is more likely to inhibit DNA polymerase than to lead to termination events upon incorporation into the DNA replication fork.

Preparation of oligodeoxynucleotides containing 5-(N-methylpiperazinyl) and 5-benzyloxymethyl uracils

Deprotected compounds 1 and 9 were allowed to react with 4,4'-dimethoxytrityl chloride in pyridine to give 5'-O-DMT nucleosides 2 and 10. The 3'-phosphoramidites 4 and 11 were incorporated into oligodeoxynucleosides (ODNs). The hybridization properties of the modified ODNs with their complementary DNA strands were studied. Interesting results were obtained when 11 was inserted as a bulged nucleoside into TWAs, duplexes, and triplexes.