164007-66-3

Upstream product

• 118188-69-5 1-(3'-cyano-2',3'-dideoxy-5'-O-trityl-β-D-erythro-pentofuranosyl)thymine 
• 146557-80-4 1-{(3'R,4'S)-5'-O-[(tert-butyl)diphenylsilyl]-2',3'-dideoxy-3'-C-(hydroxymethyl)-β-pentofuranosyl}thymine 
• 146557-69-9 1-[5-(tert-butyldiphenylsilyl)-2,3-dideoxy-3-C-(formyl)-β-D-erythro-pentofuranosyl]thymine 
• 7791-71-1 5'-O-tritylthymidine 
• 25442-44-8 1-(3'-iodo-2',3'-dideoxy-5'-O-trityl-β-D-erythro-pentofuranosyl)thymine 
• 40615-36-9 4,4'-dimethoxytrityl chloride 
• 166955-35-7 3'-Deoxy-3'-C-(acetoxymethyl)thymidine 
• 166955-34-6 5'-O-(tert-butyldiphenylsilyl)-3'-deoxy-3'-C-(acetoxymethyl)-thymidine 
• 183064-10-0 Acetic acid (2S,3R,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydro-2H-pyrimidin-1-yl)-2-trityloxymethyl-tetrahydro-furan-3-ylmethyl ester 
• 146604-41-3 1-((2R,4R,5S)-4-Hydroxymethyl-5-trityloxymethyl-tetrahydro-furan-2-yl)-5-methyl-1H-pyrimidine-2,4-dione 

Downstream Products

• 164007-67-4 5'-O-dimethoxytrityl-3'-hydroxymethyl-3'-deoxy-thymidine 

Relevant academic research and scientific papers

Bifunctional nucleosides, oligomers thereof, and methods of making and using the same

Disclosed are novel bifunctional nucleoside analogs and oligonucleosides of 3-4 bases (trimers and tetramers) and longer containing at least two consecutive internucleoside linkages of two carbon-one nitrogen atom or two carbon-one oxygen atom (3'-NCC-5',

Oligodeoxynucleotides with extended 3′- and 5′-homologous internucleotide linkages

3′-Deoxy-3′-C-(hydroxymethyl)thyrnidine (3′-DHMT) and 5′-deoxy-5′-C-(hydroxymethyl)thymidine (5′-DHMT) have been prepared and used for the synthesis of novel oligodeoxynucleotides containing extended internucleotide linkages. Enzymatic stability toward exonuclease III degradation was studied and hybridization properties were tested. The extended 3′-homologous DNA causes complete cessation of exonuclease III degradation while the extended 5′-homologous DNA shows only some decrease in degradation. Duplexes having extended internucleotide linkages show a minor decrease in hybridization stability. Triplex formation with 20-mer duplexes at pH 5.5 and high salt concentration gave almost no decrease in binding affinity when compared with unmodified triplex formation. UV experiments were also performed with oligodeoxynucleotides containing hairpin structures and bulged bases. Extended linkages in the oligodeoxynucleotides gave a small increase in Tm with sequences containing a loop, but no change or only a small decrease was observed when an extra thymidine nucleotide was incorporated in the complementary strand. Acta Chemica Scandinavica 1997.

Synthesis of 5'-phosphonate linked thymidine deoxyoligonucleotides

5'-Deoxy-5'-phosphonothymidine was synthesized and coupled with 3'-deoxy-3'-hydroxy-methylthymidine to yield a 3'-C-O-P-5' linked thymidine dinucleotide. This dimer as its 3'-phosphoramidite was used to synthesize deoxyoligonucleotides.

An extended phosphate linkage: Synthesis, hybridization and modeling studies of modified oligonucleotides

Novel stretched oligonucleotides (A-D) containing a 3'-α-C-methylene phosphodiester bridge (5-atoms long) have been synthesized on an automated synthesizer utilizing phosphoramidite chemistry. The key building-block 1- [3''-O-β-cyanoethyldiisopropylaminophosphiryl-2,3-dideoxy-5-O- dimethoxytriphenylmethyl-3-C-(hydroxymethyl)-β-D-erythro- pentofuranosyl]thymine (21) was prepared in a stereoselective manner from thymidine. Hybridization studies indicated a drop (1.8-3.0 °C/mod.) in affinity for the complementary RNA and DNA targets. Molecular modeling results indicated that the 5-atom modified backbone had a different geometry around the phosphodiester linkage compared to the natural phosphodiester linkage. The stretched backbone may not be useful for antisense or triplex constructs, however it may find applications in biochemical/enzyme studies.