139244-40-9

Upstream product

• 4836-13-9 N₄-benzoyl-2'-deoxycytidine 
• 58479-61-1 tert-butylchlorodiphenylsilane 
• 951-77-9 2'-Deoxycytidine 
• 93-97-0 benzoic acid anhydride 
• 276870-95-2 4-amino-1-((2R,4S,5R)-5-(((tert-butyldiphenylsilyl)oxy)methyl)-4-hydroxytetrahydrofuran-2-yl)pyrimidin-2(1H)-one 
• 98-88-4 benzoyl chloride 

Downstream Products

• 149097-52-9 diethyl N⁴-benzoyl-5'-O-tert-butyldiphenylsilyl-2'-deoxy-3'-O-phosphonomethylcytidine 
• 181423-12-1 N⁴-benzoyl-1-[5-O-tert-butyldiphenylsilyl-3-O-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)-2-deoxy-β-D-ribofuranosyl]-cytosine 
• 139244-41-0 N-{1-[5-(tert-butyl-diphenyl-silanyloxymethyl)-4-oxo-tetrahydro-furan-2-yl]-2-oxo-1,2-dihydro-pyrimidin-4-yl}-benzamide 
• 305819-96-9 4-N-benzoyl-1-(5-O-tert-butyldiphenylsilyl-2-deoxy-3-C-phosphono-β-D-threo-pentofuranosyl)cytosine 
• 132062-98-7 4-N-benzoyl-2'-deoxy-5'-O-phosphonomethyl-3'-O-(tetrahydro-2H-pyran-2-yl)cytidine diethyl ester 
• 132062-97-6 4-N-benzoyl-2'-deoxy-3'-O-(tetrahydro-2H-pyran-2-yl)cytidine 
• 181423-22-3 N⁴-benzoyl-1-[3-O-(2,3,5-tri-O-benzoyl-β-D-ribofuranosyl)-2-deoxy-β-D-ribofuranosyl]-cytosine 
• 195247-28-0 3-N-benzoyl-3'-O-(9-phenylxanthen-9-yl)-2'-deoxycytidine 
• 140712-80-7 N⁴-benzoyl-3'-O-dimethoxytrityl-2'-deoxycytidine 
• 854389-81-4 {(2R,3S,5R)-5-(4-Benzoylamino-2-oxo-2H-pyrimidin-1-yl)-3-[bis-(4-methoxy-phenyl)-phenyl-methoxy]-tetrahydro-furan-2-ylmethoxymethyl}-phosphonic acid monomethyl ester 

Relevant academic research and scientific papers

NUCLEOTIDE CLEAVABLE LINKERS AND USES THEREOF

Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof for sequencing a nucleic acid.

THERMALLY-CLEAVABLE PROTECTING AND LINKER GROUPS

The present invention relates to chemical linkers and protecting groups, compounds and compositions containing the chemical linkers or protecting groups, and intermediates and processes that can be used to prepare them. The chemical linkers and protecting groups are based on pyrrolidine and piperidine activating groups, which undergo intramolecular cyclisation upon heating with release of carbon dioxide, thereby releasing the organic compound from a substrate. In particular, those chemical linkers and protecting groups are useful in the solid phase synthesis of oligonucleotides according to the following representative schemes.

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.

Solid-phase synthesis of branched RNA and branched DNA/RNA chimeras

An effective method for synthesising branched oligonucleotides on solid phase in the 5' to 3' direction has been developed. Special branch-point monomers enable the synthesis of branched oligonucleotides which can have sequences of different length and base composition attached to the 2'- and 3'-hydroxyl groups of the branch point ribonucleoside. The branched oligonucleotides are assembled on commercial DNA synthesisers, the crude products are readily purified by reversed phase HPLC and the fully deprotected products are conveniently analysed by mass spectrometry.

Ribosylation of pyrimidine 2'-deoxynucleosides

The previously developed method for the preparation of 2'-O-D- ribofuranosyl-nucleosides is extended to ribosylation of 2'- deoxynucleosides. The scope and limitations of this reaction are discussed.

SYNTHESIS OF 5'-O-PHOSPHONOMETHYL DERIVATIVES OF PYRIMIDINE 2'-DEOXYNUCLEOSIDES

Reaction of sodium salt of 3-N,3'-O-bis(benzyloxymethyl)-2'-deoxyuridine (X) and 3-N,3'-O-bis(benzyloxymethyl)-2'-deoxythymidine (XI) with diethyl p-toluenesulfonyloxymethanephosphonate in dimethylformamide afforded diesters of the respective 5'-O-phospho