Reliable chemical synthesis of oligoribonucleotides (RNA) with 2'-O-[(triisopropylsilyl)oxy]methyl(2'-O-tom)-protected phosphoramidites

A method for the introduction of the 2'-O-[(triisopropylsilyl)oxy]methyl (=tom) group into N-acetylated, 5'-O-dimethoxytritylated ribonucleosides is presented. The corresponding 2'-O-tom-protected phosphoramidite building blocks were obtained in pure form and were successfully employed for the routine synthesis of oligoribonucleotides on DNA synthesizers. Under DNA coupling conditions (2.5 min coupling time for a 1.5-mmol synthesis scale) and with 5-(benzylthio)-1H-tetrazole (BTT) as activator. 2'-O-tom-protected phosphoramidites exhibited av. coupling yields >99.4%. The combination of N-acetyl and 2'-O-tom protecting groups allowed a reliable and complete two-step deprotection, first with MeNH2 in EtOH/H2O and then with Bu4NF in THF, without concomitant destruction of the product RNA sequences. [on SciFinder (R)]

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2001
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https://infoscience.epfl.ch/record/80649?ln=fr

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vignette|Structure tridimensionnelle d'un ARN régulateur (riboswitch). vignette|Structure moléculaire de l'ARN. L'acide ribonucléique ou ARN (en anglais, RNA, pour ribonucleic acid) est un acide nuc

Une synthèse chimique est un enchaînement de réactions chimiques mis en œuvre volontairement ou non permettant l'obtention d'un ou de plusieurs produits finaux, parfois avec isolation de composés chim

La synthèse d'oligonucléotide est la synthèse chimique de fragments relativement courts d'acide nucléique avec une structure définie. Principe La technique est largement utilisée dans les

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3'-Deoxyribopyranose (4' -> 2')-oligonucleotide duplexes (=p-DNA duplexes) as substitutes of RNA hairpin structures

Damian Ackermann

By automated synthesis, we prepd. hybrid oligonucleotides consisting of covalently linked RNA and p-DNA sequences (p-DNA = 3'-deoxyribopyranose (4'->2')-oligonucleotides). The pairing properties of corresponding hybrid duplexes formed from fully complementary single strands were investigated. An uninterrupted p-p-stacking at the p-DNA/RNA interface and cooperative pairing between the two systems was achieved by connecting them via a 4'-p-DNA-2'->5'-RNA-3' and 5'-RNA-2'->4'-p-DNA-2' phosphodiester linkage, resp. The RNA 2'-phosphoramidites required for the formation of the RNA-2'->4'-p-DNA phosphodiester linkage were synthesized from the corresponding, 3'-O-tom-protected ribonucleosides (tom = [(triisopropylsilyl)oxy]methyl). Analogs of the FMN binding aptamer and the hammerhead ribozyme were prepd. Each of these analogs consisted of two p-DNA/RNA hybrid single strands with complementary p-DNA sequences, designed to substitute stem/loop and stem motifs within the parent compds. By comparative binding and cleavage studies, it was found that mixing of the two complementary p-DNA/RNA hybrid sequences resulted in the formation of the fully functional analogs of the FMN-binding aptamer and of the hammerhead ribozyme, resp. [on SciFinder (R)]

2002

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Fast and reliable automated synthesis of RNA and partially 2'-O-protected precursors ("caged RNA") based on two novel, orthogonal 2'-O-protecting groups

Damian Ackermann

Two sets of RNA phosphoramidites, carrying the (fluoride-labile) 2'-O-[(triisopropylsilyl)oxy]methyl (tom) group and the (photolabile) [(R)-1-(2-nitrophenyl)ethoxy]methyl ((R)-npeom) group, were prepd. The two protecting groups were completely orthogonal to each other. Three ribozyme-substrate constructs, protected each by a (R)-npeom group, were synthesized; on photolysis, efficient cleavage of this remaining protecting group occurred. It could be demonstrated that the presence of one (R)-npeom group within a RNA strand has only a minor influence on the pairing properties of corresponding duplexes. [on SciFinder (R)]

1999

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Synthesis of 2'-O-[(triisopropylsilyl)oxy]methyl(=tom)-protected ribonucleoside phosphoramidites containing various nucleobase analogs

Sébastien Porcher

The first results of a study aiming at an efficient prepn. of a large variety of 2'-O-[(triisopropylsilyl)oxy]methyl(=tom)-protected ribonucleoside phosphoramidite building blocks contg. modified nucleobases are reported. All of the here presented nucleosides have already been incorporated into RNA sequences by several other groups, employing 2'-O-tbdms- or 2'-O-tom-protected phosphoramidite building blocks (tbdms=(tert-butyl)dimethyl-silyl). We now optimized existing reactions, developed some new and shorter synthetic strategies, and sometimes introduced other nucleobase-protecting groups. The 2'-O-tom, 5'-O-(dimethoxytrityl)-protected ribonucleosides N2-acetyl-iso-cytidine, O2-(diphenyl-carbamoyl)-N6-isobutyryl-isoguanosine, N6-isobutyryl-N2-(methoxy-acetyl)purine-2,6-diamine ribonucleoside (=N8-isobutyryl-2-[(methoxyacetyl)amino]adenosine), 5-methyluridine, and 5,6-dihydro-uridine were prepd. by first introducing the nucleobase protecting groups and the dimethoxytrityl group, resp., followed by the 2'-O-tom group. The other presented 2'-O-tom, 5'-O-(dimethoxytrityl)-protected ribonucleosides inosine, 1-methyl-inosine 18, N6-iso-pent-2-enyl-adenosine, N6-methyl-adenosine, N6,N6-dimethyl-adenosine, 1-methyl-guanosine, N2-methylguanosine, N2,N2-dimethyl-guanosine, N6-(chloroacetyl)-1-methyladenosine, N6-(1S,2R)-2-[(tert-butyl)dimethyl-silyl]oxy-1-[2-(4-nitrophenyl)ethoxy]carbonylpropylamino carbonyl-adenosine (derived from L-threonine) and N4-acetyl-5-methyl-cytidine were prepd. by nucleobase transformation reactions from std., already 2'-O-tom-protected. Finally, all these nucleosides were transformed into the corresponding phosphoramidites, which are fully compatible with the assembly and deprotection conditions for std. RNA synthesis based on 2'-O-tom-protected monomeric building blocks. [on SciFinder (R)]

2005

Chargement

La synthèse d'oligonucléotide est la synthèse chimique de fragments relativement courts d'acide nucléique avec une structure définie. Principe La technique est largement utilisée dans les

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