28854-96-8

Upstream product

• 4784-41-2 1-(2-deoxy-3,5-di-O-p-toluoyl-α-D-erythro-pentofuranosyl)thymine 
• 35898-26-1 4-Methyl-benzoic acid (2R,3S,5S)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethyl ester 
• 3056-13-1 3',5'-di-O-p-toluoyl-α-2'-deoxythymidine 
• 4449-31-4 1-[O³,O⁵-bis-(4-chloro-benzoyl)-α-D-erythro-2-deoxy-pentofuranosyl]-5-methyl-1H-pyrimidine-2,4-dione 
• 50-89-5 thymidine 
• 153737-54-3 3'-5'-di-O-acetyl-α-D-thymidine 
• 444810-96-2 3'-O-diphenylacetyl-β-thymidine 
• 4449-39-2 3',5'-di-O-toluoylthymidine 
• 21740-23-8 3,5-O-bis(4-chlorobenzoyl)-2-deoxy-α-D-ribofuranosyl chloride 
• 65-71-4 thymin 
• 7288-28-0 2,4-bis(trimethylsiloxy)-5-methylpyrimidine 
• 3056-13-1 3',5'-di-O-p-toluoyl-2'-deoxythymidine 
• 676598-19-9 methyl 2-deoxy-5-O-(4-methylbenzoyl)-D-erythro-pentofuranoside 
• 78138-12-2 4-Methyl-benzoic acid (2R,3S)-3-benzyloxy-5-chloro-tetrahydro-furan-2-ylmethyl ester 

Downstream Products

• 104766-16-7 5'-O-(4,4'-dimethoxytrityl)-α-thymidine 
• 201219-77-4 5'-O-acetyl-3'-O-(4,4'-dimethoxytrityl)-α-thymidine 
• 152581-54-9 5'-O-dimethoxytrityl-3'-O-(tert-butyldimethylsilyl)-α-thymidine 
• 114988-00-0 Phosphoramidous acid (2R,3S,5S)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester methyl ester 
• 28854-96-8 C₁₀H₁₄N₂O₅ 
• 13410-30-5 2-(2-deoxy-β-D-erythro-pentofuranosyl)-6-methyl-1,2,4-triazine-3,5(2H,4H)-dione 
• 2642-43-5 thymidine 3'-monophosphate 
• 2863-04-9 Thymidine 3',5'-diphosphate 
• 56822-33-4 3',5'-di-O-mesylthymidine 
• 15981-92-7 2,3'-anhydrothymidine 
• 78582-15-7 4-chloro-1-(2'-deoxy-β-D-erythro-pentofuranosyl)-1H-imidazo<4,5-c>pyridine 
• 111160-28-2 1-(5-chloro-2,5-dideoxy-β-D-erythro-pentofuranosyl)-5-methyl-4-(1,2,4-triazol-1-yl)pyrimidin-2(1H)-one 
• 109389-25-5 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methyl-4-(1H-1,2,4-triazol-1-yl)pyrimidin-2(1H)-one 
• 90029-85-9 3-(3-oxoprop-1-enyl)thymidine 

Relevant academic research and scientific papers

Tri-O-acyl 2-deoxy-D-ribofuranose: An effective enzyme-assisted one-pot synthesis from 2-deoxy-D-ribose and transformation into 2′-deoxynucleosides

Regioselective lipase-catalyzed (Novozym 435 from Candida antartica) acylations of unprotected 2-deoxy-D-ribose and D-ribose, by use of propionic anhydride, afforded the novel 5-0-monoacylated derivatives 1 and 4, respectively. Subsequent addition of acetic anhydride and pyridine into the reaction mixtures gave the corresponding per-0-acylated pentofuranoses 2 and 5 in almost quantitative overall yields from the unprotected carbohydrates. The versatility of compound 2 as an universal synthon for synthesis of anomeric mixtures of 2′-deoxynucleosides is demonstrated.

Active species for Ce(IV)-induced hydrolysis of phosphodiester linkage in cAMP and DNA

The hydrolysis of cyclic adenosine 3′,5′-monophosphate and 2′-deoxythymidylyl(3′-5′)2′-deoxythymidine by Ce(NH 4)2(NO3)6 was kinetically studied. The rate of hydrolysis was fairly proportional to the concentration of [Ce 2IV (OH)4]4+, showing that this is the catalytically active species. According to quantum-chemical calculation, the two Ce(IV) ions in this [Ce2IV (OH)4] 4+ cluster are bridged by two OH residues. Upon the complex formation with H2PO4- (a model compound for the phosphodiesters), these two Ce(IV) ions bind the two oxygen atoms of the substrate and enhance the electrophilicity of the phosphorus atom. The catalytic mechanism of Ce(IV)-induced hydrolysis of phosphodiesters has been proposed on the basis these results. Copyright Taylor & Francis Group, LLC.

THE USE OF ZINC BROMIDE FOR REMOVAL OF DIMETHOXYTRITYL ETHERS FROM DEOXYNUCLEOSIDES

Zinc bromide has been observed to detritylate specifically 5'-trityldeoxy-deoxynucleosides whereas 3'-trityl ethers are not cleaved.Of additional practical consideration and in contrast to protic acids, no depurination was observed with this reagent.

Sensitized two-photon photochemical deprotection

The photoremovable protecting group NPPoc has little sensitivity to two-photon excitation, limiting its use in applications requiring high spatial control of its photochemistry. In the presence of a triplet sensitizer with a large two-photon absorption cross-section, however, the two-photon uncaging action cross-section is improved to levels useful in a variety of applications.

Synthesis of thymidine from 5-iodo-2'-deoxyuridine

A simple, high yield synthesis of thymidine from 5-iodo-2'-deoxyuridine is described, using tetramethyltin and tetrakis(triphenylphosphine)palladium(0) in hexamethylphosphoric triamide. Likewise, 5-phenyl- and 5-vinyl-2'-deoxyuridine can be obtained, and through reduction of the latter the 5-ethyl analogue is also at hand.

Synthesis and stereochemical assignment of DNA spore photoproduct analogues

Investigation of the DNA repair process performed by the spore photoproduct (SP) lyase repair enzyme is strongly hampered by the lack of defined substrates needed for detailed enzymatic studies. The problem is particularly severe because the repair enzyme belongs to the class of strongly oxygen-sensitive radical (S)-adenosyl-methionine (SAM) enzymes, which are notoriously difficult to handle. We report the synthesis of the spore photoproduct analogues 1a and 1b, which have open backbones and are diastereoisomers. In order to solve the problem of stereochemical assignment, two further derivatives 2a and 2b with closed backbones were prepared. The key step of the synthesis of 2a/b is a metathesis-based macrocyclization that strongly increases the conformational rigidity of the synthetic spore photoproduct derivatives. NOESY experiments of the cyclic isomers furnished a clear cross-peak pattern that allowed the unequivocal assignment of the stereochemistry. The results were transfer red to the data for isomers 1a and 1b, which were subsequently used for enzymatic-repair studies. These studies were performed with the novel spore photoproduct lyase repair enzyme from Geobacillus stearothermophilus. The studies showed an accordance with a recent investigation performed by us with the spore photoproduct lyase from Bacillus subtilis,[1] in that only the 5 isomer la is recognized and repaired. The ability to prepare a defined functioning substrate now paves the way for detailed enzymatic studies of the SP-lyase lesion recognition and repair process.

1:1 and 1:2 complexes of Bu4NF and BF3·Et2O: Unique properties as reagents for cleavage of silyl ethers

A new method for removal of trialkylsilyl groups from silyl ethers using Complex A and Complex B, generated from tetrabutylammonium fluoride (TBAF) and BF3·Et2O has been developed. The desilylation by use of these boron complexes is significantly affected by the steric factor on the Si atom and the reagent.

New acid photogenerators based on thioxanthen-9-one sulfonium derivatives for detritylation in the oligonucleotide synthesis

Photochemical activity of a number of cationic thioxanthen-9-one derivatives for the formation of the trityl cation was studied, which resulted in the selection of compounds suitable for photodetritylation. 10-(4-Heptyloxyphenyl)-9-oxo-2-(N,N,N-triethylammonio)methyl-9H-thioxanthenium bis(hexafluorophosphate) and 2-methyl-, 2-(2-methyl-1-propanoyl-2-tosyl)-, 1-chloro-4-propoxy-, and 2,4-diethyl-10-(4-heptyloxyphenyl)-9-oxo-9H- thioxanthenium hexafluorophosphates were found to be photoactivators of detritylation of 5′-O-(4,4′-dimethoxytrityl)thymidine. The detritylation reaction is the most efficient in dichloromethane. 2,4-Diethyl-10-(4-heptyloxyphenyl)-9-oxo-9H-thioxanthenium hexafluorophosphate was used as a detritylation photoactivator in the oligonucleotide synthesis using an automated DNA synthesizer. The yield in the elongation step of the oligonucleotide chain was 98%.

Tuning the stability of alkoxyisopropyl protection groups

Five different 2-alkoxypropan-2-yl groups are introduced as acid-labile protecting groups for the 5’- and 3’-hydroxy groups of a 2’-deoxynucleoside. All studied protecting groups were readily introduced with good to excellent yields using the appropriate enol ether as a reagent and 0.5 to 1 mol % p-toluenesulfonic acid as a catalyst. The protected compounds could be purified by silica gel column chromatography without degradation. The compatibility of these protecting groups in parallel use with benzoyl and silyl groups was verified. The stabilities of the different alkoxy acetal protecting groups were compared by following the kinetics of their hydrolysis at 25.0 °C in buffered solutions through an HPLC method. In the pH range 4.94 to 6.82 the hydrolysis reactions are of first order in the hydronium ion. The rate of hydrolysis correlates with the electron-donating or electron-withdrawing ability of the corresponding alkoxy group. The studied 2-alkoxypropan-2-yl groups and the relative rate constants for their cleavage from the 5’-hydroxy group of 2’-deoxythymidine were: cyclohexyloxy (krel = 7.7), isopropoxy (7.4), methoxy (1), benzyloxy (0.6) and 2,2,2-trifluoroethyloxy (0.04). The attachment of the same groups to the 3’-hydroxy group are from 1.3 to 1.9-fold more stable. The most reactive of these acetone-based acetal groups are faster removed than a dimethoxytrityl group, and they are easier to cleave completely in solution. The structural variation allows steering of the stability and lipophilicity of the compounds in some range.

DIALKYL ALUMINIUM CHLORIDE: A REAGENT FOR REMOVAL OF TRITYL GROUP FROM TRITYL ETHERS OF DEOXYNUCLEOSIDES, DEOXYNUCLEOTIDES, AND OLIGODEOXYNUCLEOTIDES

Detritylation of N-acyl-5'-O-tritylated deoxynucleosides, deoxynucleotides, and oligodeoxynucleotides have been quantitatively achieved in minutes at room temperature by using diethylaluminium chloride or diisobutylaluminium chloride.Reactions take place in unpolar solvents in homogeneous phase under completely aprotic conditions.