Synthesis of inosine 6-phosphate diesters via phosphitylation of the carbonyl oxygen

Inosine derivatives bearing a phosphodiester group at the O(6)-position of the nucleobase were synthesized via phosphitylation of the carbonyl oxygen using phosphoramidites activated by non-nucleophilic acidic activators.

Universal 2-(4-nitrophenyl)ethyl and 2-(4-nitrophenyl)ethoxycarbonyl protecting groups for nucleosides and nucleotides

A universal blocking group strategy for nucleobases is described, using the 2-(4-nitrophenyl)ethyl (NPE) group for O4-T-, O4-U-, O6-dG-, and O6-G-protection as well as the 2-(4-nitrophenyl)ethoxycarbonyl (NPEOC) group for amino protection in dC, C, dA, A, dG, and G. Conversion into the corresponding 5'-O-dimethoxytrityl derivatives and subsequent phosphitylation to form the fully protected 3'-O-(2-cyanoethyl-N,N-diisopropylphosphoramidites) and 3'-O-(2-(4-nitrophenyl)ethyl-N,N-diisopropylphosphoramidites) produces a new class of interesting building blocks for oligonucleotide synthesis.

A general method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides having promising hybridization affinity for DNA and RNA and enhanced nuclease resistance

[reaction: see text] An effective method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides as a new class of 2'-O-modified RNAs was developed. The reaction of appropriately protected ribonucleoside derivatives with acrylonitrile in t-BuOH in the presence of Cs2CO3 gave 2'-O-cyanoethylated ribonucleoside derivatives in excellent yields, which were converted by a successive selective deprotection/protection strategy to 2'-O-cyanoethylated 5'-O-dimethoxytritylribonucleoside 3'-phosphoramidite derivatives in high yields. Fully 2'-O-cyanoethylated oligoribonucleotides, (Uce)12 and (GceAceCceUce)3, were successfully synthesized in the phosphoramidite approach by use of the phosphoramidite building blocks. It was also found that oligoribonucleotides having a 2'-O-cyanoethylated ribonucleoside (Uce, Cce, Ace, or Gce) could be obtained by the selective removal of the TBDMS group from fully protected oligoribonucleotide intermediates without loss of the cyanoethyl group by use of NEt3 x 3HF as a desilylating reagent. The detailed T(m) experiments revealed that oligoribonucleotides containing 2'-O-cyanoethylated ribonucleosides have higher hybridization affinity for both DNA and RNA than the corresponding unmodified and 2'-O-methylated oligoribonucleotides. In addition, introduction of a cyanoethyl group into the 2'-position of RNA resulted in significant increase of nuclease resistance toward snake venom and bovine spleen phosphodiesterases compared with that of the methyl group.

Functionalization of guanosine and 2'-deoxyguanosine at C6: a modified Appel process and S(N)Ar displacement of imidazole

Treatment of sugar-protected 2-N-trityl derivatives of guanosine and 2'-deoxyguanosine with imidazole/triphenylphosphine/iodine/ethyldiisopropylamine gives the corresponding 6-(imidazol-1-yl)-2-(tritylamino)purine nucleosides. S(N)Ar displacement of the imidazole moiety with nucleophiles provides 2-amino-6-substituted-purine nucleosides and 2'-deoxynucleosides.

New methods for the synthesis of N-benzoylated uridine and thymidine derivatives; a convenient method for N-debenzoylation

An improved procedure for the synthesis of N-benzoyl-2',3'-O-isopropylidene uridine via one-step selective N-benzoylation of 2',3' -O-isopropylidene uridine has been developed. An efficient synthetic route to N-benzoyl thymidine via initial tribenzoylation, followed by selective hydrolysis of the benzoates is also described. De-N-benzoylation of N-benzoylated thymidine and uridine derivatives can be conveniently effected under neutral conditions, by heating with benzyl alcohol.

Mild and efficient functionalization at C6 of purine 2'-deoxynucleosides and ribonucleosides

[reaction: see text] Treatment of sugar-protected inosine and 2'-deoxyinosine derivatives with a cyclic secondary amine or imidazole and I(2)/Ph(3)P/EtN(i-Pr)(2)/(CH(2)Cl(2) or toluene) gave quantitative conversions into 6-N-(substituted)purine nucleosides. S(N)Ar reactions with 6-(imidazol-1-yl) derivatives gave 6-(N, O, or S)-substituted products. The 6-(benzylsulfonyl) group underwent S(N)Ar displacement with an arylamine at ambient temperature.

Synthesis of 4-thiouridine, 6-thioinosine, and 6-thioguanosine 3',5'-O-bisphosphates as donor molecules for RNA ligation and their application to the synthesis of photoactivatable TMG-capped U1 snRNA fragments

4-Thiouridine, 6-thioguanosine, and 6-thioinosine 3',5'-bisphosphates (9, 20, and 28) were synthesized in good yields by considerably improved methods. In the former two compounds, uridine and 2-N-phenylacetylguanosine were converted via transient O-trimethylsilylation to the corresponding 4- and 6-O-benzenesulfonyl intermediates (2 and 13), which, in turn, were allowed to react with 2-cyanoethanethiol in the presence of N-methylpyrrolidine to give 4-thiouridine (3) and 2-N-phenylacetyl-6-thioguanosine derivatives (14), respectively. In situ dimethoxytritylation of these thionucleoside derivatives gave the 5'-masked products 4 and 15 in high overall yields from 1 and 11. 6-S-(2-Cyanoethyl)-5'-O-(4,4'-dimethoxytrityl)-6-thioinosine (23) was synthesized via substitution of the 5'-O-tritylated 6-chloropurine riboside derivative 22 with 2-cyanoethanethiol. These S-(2-cyanoethyl)thionucleosides were converted to the 2'-O-(tert-butyldimethylsilyl)ribonucleoside 3'-phosphoramidite derivatives 7, 18, and 26 or 3',5'-bisphosphate derivatives 8, 19, and 27. Treatment of 8, 19, and 27 with DBU gave thionucleoside 3',5'-bisphosphate derivatives 9, 20, and 28, which were found to be substrates of T4 RNA ligase. These thionucleoside 3',5'-bisphosphates were examined as donors for ligation with m3(2,2,7) G5'pppAmUmA, i.e., the 5'-terminal tetranucleotide fragment of U1 snRNA, The 4-thiouridine 3',5'-bisphosphate derivative 9 was found to serve as the most active substrate of T4 RNA ligase with a reaction efficiency of 96%.

Nucleic Acid Related Compounds. 105. Synthesis of 2',3'-Didehydro-2',3'-dideoxynucleosides from Ribonucleoside Cyclic 2',3'-(Sulfates or Phosphates) or 2',3'-Dimesylates via Reductive Elimination with Sodium Naphthalenide(1)

Treatment of purine ribonucleosides with thionyl fluoride resulted in formation of cyclic 2',3'-sulfite esters. Acetylation of the 5'-hydroxy group and Sharpless oxidation (NaIO(4)/RuCl(3)) gave the cyclic 2',3'-sulfate ester derivatives. Treatment of 5'-O-silyl-protected ribonucleosides with thionyl chloride followed by oxidation gave an alternative route to the cyclic 2',3'-sulfates. Reductive elimination with sodium naphthalenide (THF/-50 degrees C) gave the 2',3'-unsaturated nucleosides. Parallel treatment of adenosine cyclic 2',3'-phosphate gave the 2',3'-olefin. The adenine, hypoxanthine, and 2-amino-6-methoxypurine 2',3'-didehydro-2',3'-dideoxynucleosides were prepared efficiently (40-60% overall yields of crystalline, analytically pure products; 3-5 steps, some combined into one-flask procedures) by treatment of 5'-O-protected 2',3'-di-O-mesylribonucleosides with sodium naphthalenide. Reactions were performed at or below ambient temperature with readily available reagents and standard laboratory conditions.