23339-47-1

Upstream product

• 21090-30-2 3'-O-acetylthymidine 
• 98796-53-3 N₆-benzoyl-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyadenosine-3'-O-[O-(2-cyanoethyl)-N,N'-diisopropylphosphoramidite] 
• 51549-39-4 N⁶-benzoyl-5′-O-(tert-butyldimethylsilyl)-2′-deoxyadenosine 
• 130974-98-0 Acetic acid (2R,3S,5R)-2-{[(2R,3S,5R)-5-(6-benzoylamino-purin-9-yl)-2-hydroxymethyl-tetrahydro-furan-3-yloxy]-hydroxy-phosphoryloxymethyl}-5-(5-methyl-2-oxo-4-[1,2,4]triazol-1-yl-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester 
• 121804-03-3 3'-acetyl-4-(1,2,4-triazol-1-yl)-thymidine 
• 80817-52-3 Phosphoric acid benzotriazol-1-yl ester (2R,3S,5R)-5-(6-benzoylamino-purin-9-yl)-2-(tert-butyl-dimethyl-silanyloxymethyl)-tetrahydro-furan-3-yl ester 2-chloro-phenyl ester 
• 426833-88-7 acetic acid 2-((2-cyano-ethoxy)-{2-hydroxymethyl-5-[6-(2-phenoxy-acetylamino)-purin-9-yl]-tetrahydro-furan-3-yloxy}-phosphoryloxymethyl)-5-(2,4-dioxo-5-phenylsulfanylmethyl-3,4-dihydro-2H-pyrimidin-1-yl)-tetrahydro-furan-3-yl ester 
• 110543-74-3 N⁶-(phenoxyacetyl)-5'-O-(p,p'-dimethoxytrityl)-2'-deoxyadenosine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite) 
• 111476-35-8 3'-O-acetyl-5-(phenylthiomethyl)-2'-deoxyuridine 
• 134817-00-8 Diisopropyl-phosphoramidous acid (2R,3S,5R)-5-(6-amino-purin-9-yl)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-tetrahydro-furan-3-yl ester methyl ester 
• 140613-55-4 2-cyanoethyl 5'-O-(4,4'-dimethoxytrityl)-2'-deoxyadenosine 3'-(N,N-diisopropyl)phosphoramidite 
• 426833-89-8 2'-deoxyadenylyl-(3'-5')-5-(phenylthiomethyl)-2'-deoxyuridine 

Relevant academic research and scientific papers

N-pent-4-enoyl nucleosides: Application in the synthesis of support-bound and free oligonucleotide analogs by the H-phosphonate approach

N-pent-4-enoyl nucleoside H-phosphonates are versatile building blocks for the synthesis of support-bound and free oligonucleotide analogs.

O-selectivity and utility of phosphorylation mediated by phosphite triester intermediates in the N-unprotected phosphoramidite method

Previously, O-selective phosphorylation on polymer supports in the N-unprotected phosphoramidite method could not be carried out because the amino groups of dA and dC have high reactivity toward tervalent phosphorus(III)-type phosphitylating reagents. In

A new strategy for the synthesis of oligodeoxynucleotides directed towards perfect O-selective internucleotidic bond formation without base protection

Deoxyadenosine and deoxycytidine have nucleophilic amino groups so that the undesired N-phosphitylation of these amino groups occurred in the previous phosphoramidite methods without base protection. We report that the N-phosphitylation could be considerably suppressed in our new HOBt-mediated coupling strategy via phosphite intermediates as reactive species. Thus, 99.7-99.9% O-selective internucleotidic bond formation was achieved.

A novel approach to oligonucleotide synthesis using an imidazolium ion tag as a soluble support

(Chemical Equation Presented) The synthesis of oligonucleotides in solution using a soluble, ionic liquid based support is described. Short oligomers of varying base composition were synthesized using this method in high yields and high purity, requiring

O-selective condensation using P-N bond cleavage in RNA synthesis without base protection

(Chemical Equation Presented) In RNA synthesis without base protection, a new method for O-selective condensation with more than 99% selectivity was developed by 6-nitro-HOBt-mediated cleavage of undesired P(III)-N bonds on nucleobase moieties. Moreover, we for the first time succeeded in synthesizing oligoRNAs without base protection.

Cross-linked thymine-purine base tandem lesions: Synthesis, characterization, and measurement in γ-irradiated isolated DNA

5-(Phenylthiomethyl)-2′-deoxyuridine has been recently shown to be a specific photolabile precursor of 5-(2′-deoxyuridilyl)methyl radical that is involved in the formation of tandem base lesion with vicinal guanine in oxygen-free aqueous solution. The thionucleoside was incorporated by either liquid or solid-phase phosphoramidite synthesis into dinucleoside monophosphates with a 2′-deoxyadenosine residue as the vicinal nucleoside located either at the 3′ or 5′-extremity. UV-C irradiation of the modified dinucleoside monophosphate under anaerobic conditions gives rise to cross-linked thymineCH2-C8adenine tandem base lesions which were isolated and characterized by 1H NMR and mass spectrometry analyses. The formation of the latter tandem lesions involved an intramolecular addition of the 5-(2′-deoxyuridilyl)methyl radical to the C8 of the adenine moiety. A sensitive and specific assay aimed at monitoring the formation of the four thymineCH2-C8purine adducts, namely d(T∧G), d(G∧T), d(T∧A), d(A∧T), within DNA, was designed. This was based on a liquid chromatography analysis coupled to tandem mass spectrometry (HPLC-MS/MS) detection of the dinucleoside monophosphates which were quantitatively released from γ-irradiated DNA and oligodeoxyribonucleotides by enzymatic hydrolysis. The four lesions were detected in both single-stranded oligodeoxyribonucleotide and isolated DNA upon exposure to γ-radiation in oxygen-free aqueous solution. It was found that the tandem guanine-thymine lesions were produced more efficiently than the adenine-thymine cross-links. Moreover, a significant sequence effect was observed. Thus, the yield of formation of the tandem lesions is higher when the purine base is located at the 5′ position of the 5-(2′-deoxyuridilyl)methyl radical.

Synthesis and nuclease stability of dinucleotides containing an anti conformationally constrained acyclic thymidine

Novel heterodimers containing an anti conformationally constrained acyclic thymidine were prepared and the nuclease resistance of the modified dinucleotides were studied.

Synthesis of 1'%,2',3',4'%,5',5"-(2)H6-β-D-ribonucleosides and 1'%,2',2",3',4'%,5',5"-(2)H7-β-D-2'-deoxyribonucleosides for Selective Suppression of Proton Resonances in Partially-deuterated Oligo-DNA, Oligo-RNA and in 2,5A core ((1)H-NMR window)

Raney nickel-(2)H2O exchange reaction on an epimeric mixture of methyl α/β-D-ribofuranoside 1 produced methyl 1%,2,3,4%,5,5'-(2)H6-α/β-D-ribofuranoside 2 ( >97 atom percent (2)H at C2, C3, C5/5'; ca. 85 atom percent (2)H at C4(C4%); ca. 20 atom percent (2)H at C1(C1%)) which was obtained in 60 - 80percent yield along with epimeric xylo and arabino by-products.Toluoylation of the crude 2 in dry pyridine and a careful separation on a column of silica gel gave pure 1-O-methyl-2,3,5-tri-O-(4-toluoyl)-α/β-D-1%,2,3,4%,5,5'-(2)H6-ribofuranoside 4 (48percent).Conversion of 4 to1-O-acetyl-2,3,5-tri-O-toluoyl-α/β-D-1%,2,3,4%,5,5'-(2)H6-ribofuranoside 6 (82percent) provided the crucial building block for the synthesis of deuterionucleosides for RNA or DNA synthesis.Compound 6 was then condensed with silyated uracil, N4-benzoylcytosine, N6-benzoyladenine, N2-acetyl-O6-diphenylcarbamoylguanine and thymine in anhydrous solvent using trimethylsilyl trifluoromethanesulfonate to give the corresponding isomerically pure 1'%,2',3',4'%,5',5"-(2)H6-ribonucleoside derivatives 7, 8, 9, 10, 11 in 75, 85, 60, 73 and 91percent yields, respectively. 1'%,2',3',4'%,5',5"-(2)H6-ribonucleosides 13-16 were converted in high yields to the corresponding 1'%,2',2",3',4'%,5',5"-(2)H7-2'-deoxynucleosides 41-44 in the following manner: 3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl (TPDS)-1'%,2',3',4'%,5',5"-(2)H6-nucleosides 29-32 were converted to the corresponding 2'-O-phenoxythiocarbonyl derivatives 33-36, which were deoxygenated by tri-n-butyltin deuteride to give 1'%,2',2",3',4'%,5',5"-(2)H7-2'-deoxynucleosides 37-40 and subsequently deprotected to give 41-44.Pure 1'%,2',3',4'%,5',5"-(2)H6-ribonucleoside derivatives 12-15, 1'%,2',2",3',4'%,5',5"-(2)H7-2'-deoxynucleoside blocks 41-44 and their natural-abundance counterparts were then used to assemble partially deuterated ribonucleotide-dimers (* indicates deuterated moiety): UpA* 77, CpG* 78, ApU* 79, GpC* 80, partially deuterated 2'-deoxyribonucleotide-dimers d(TpA*) 93, d(CpG*) 94, d(ApT*) 95, d(GpC*) 96 and partially deuterated 2,5A core (A*2'p5'A2'p5'A*) (109).These nine partially deuterated oligonucleotides were subsequently compared with their corresponding natural-abundance counterparts by 500 MHz (1)H-NMR spectroscopy to evaluate the actual NMR simplifications achieved in the non-deuterated part ((1)H-NMR window) as a result of specific deuterium incorporation.Detailed 1D (1)H-NMR (500 MHz), 2D correlation spectra (DQF-COSY and TOCSY), T1 measurements for (1)H-, (13)C- and INEPT (13)C-NMR spectra have been presented and discussed to assess the utility of stereospecific deuterium incorporation to create the (1)H- or (13)C-NMR window.

A NEW APPROACH TO THE SYNTHESIS OF PHOSPHOTRIESTER INTERMEDIATES OF NUCLEOSIDES AND NUCLEIC ACIDS

Aryl phosphorodichloridates can be converted by means of 1-hydroxybenzotriazole into an effective phosphorylating agent, which can be applied to the synthesis of phosphotriester intermediates of nucleic acids.