304849-85-2

Upstream product

• 40615-36-9 4,4'-dimethoxytrityl chloride 
• 19083-35-3 5-(benzyloxy)methyl-2′-deoxyuridine 
• 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 
• 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 
• 7226-75-7 5-benzyloxymethyl-3',5'-di-O-toluoyl-2'-deoxyuridine 
• 98808-20-9 O,O'-bis(trimethylsilyl)-5-benzyloxymethyluracil 
• 4330-34-1 methyl 3,5-di-O-toluoyl-2-deoxy-D-ribofuranose 

Downstream Products

• 304849-87-4 5-benzyloxymethyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 3'-(N,N-diisopropyl)-2-cyanoethyl phosphoramidite 

Relevant academic research and scientific papers

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.

Aromatic vs. Carbohydrate residues in the major groove: Synthesis of 5-[(benzyloxy)methyl]pyrimidine nucleosides and their incorporation into oligonucleotides

The synthesis of 5-[(benzyloxy)methyl]-substituted pyrimidine 2'-deoxynucleosides 14 and 15 starting from the uracil derivative 6 and tetra-O-acetyl-D-ribose is described (Schemes 1-3). These nucleosides were converted to the corresponding cyanoethyl phosphoramidites 18 and 19, respectively, and incorporated into oligodeoxynucleotide decamers. The 5-[(benzyloxy)methyl]-nucleoside building blocks (bo)T(d) and (bom)C(d) (bo = benzyloxy, bom = (benzyloxy)methyl) - shape analogs of the naturally occurring glucosylated nucleosides 1 and 2 (see Fig. 1) - lead to weaker binding affinities of oligodeoxynucleotides pairing to DNA as well as RNA complements. The modification is more destabilizing in the case of (bo)T(d) than (bom)C(d). Analysis of the thermodynamics of duplex formation shows that (bo)T(d) and (bom)C(d) incorporation leads to a smaller entropy change in duplex formation that is, however, overcompensated by a less favorable enthalpy term. Molecular-modeling studies suggest that the benzyl groups reside in the major groove which would explain the improved pairing entropy as a result of the exclusion of ordered H2O.