A new method for the synthesis of branched ribonucleotides

Highly efficient chemical synthesis of 2′-O-methyloligoribonucleotides and tetrabiotinylated derivatives; novel probes that are resistant to degradation by RNA or DNA specific nucleases

“…spectrum (CDC13) 6: 163.63 (C4), 157.78 (carbonyl of trifluoroacetyl), 156.64 (C-2), 138.71 (C-6), 115.90 (CF3), 95.75 (C-5), 87.06 (C-i'), 85.32 (C4'), 70.62 (C-3'), 62.05 (C-5'), 41.76, 40. 16 and 39.35 (-NH-CH2, C-2' and CH2-NH-CO), 27.98, 27.38 and 23.53 (C4, 2 and 3 of pentyl), 25.64 and 25.48 (CH3s of t-Bu), 18.04 and 17.71 (quaternary Cs of t-Bu), -4.86, -5.12, -5.74 and -5.80 p.p.m. (Si-CH3s).…”

Synthetic Strategies and Parameters Involved in the Synthesis of Oligodeoxyribonucleotides According to the Phosphoramidite Method

“…Reagents other than 1H-tetrazole have also been used to activate deoxyribonucleoside phosphoramidites, including N-methylimidazolium trifluoromethanesulfonate (Arnold et al, 1989); N-methylimidazole hydrochloride (Hering et al, 1985); pyridinium tetrafluoroborate (Brill et al, 1991); pyridinium chloride, pyridinium bromide, and pyridinium 4-methylbenzinesulfonate (Beier and Pfleiderer, 1999); N-methylanilinium trifluoroacetate (Fourrey and Varenne, 1984); N-methylanilinium trichloroacetate (Fourrey et al, 1987); benzimidazolium triflate (Hayakawa et al, 1996); imidazolium triflate (Hayakawa and Kataoka, 1998); pyridine hydrochloride/imidazole (Gryaznov and Letsinger, 1992); 5-trifluoromethyl-1H-tetrazole (Hering et al, 1985); 5-(4-nitrophenyl)-1H-tetrazole (Froehler and Matteucci, 1983); 5-(2-nitrophenyl)-1H-tetrazole (Pon, 1987;Montserrat et al, 1994); 1-hydroxybenzotriazole (Claesen et al, 1984); 2,4,5-tribromo-and 2-nitro-imidazoles (Xin and Just, 1996); benzotriazole and 5-chlorobenzotriazoles (Xin and Just, 1996); and 4,5dichloro-, 2-bromo-4,5-dicyano-, and 4,5-dicyano-imidazoles (Xin and Just, 1996). 5-Ethylthio-and 5-benzylthio-1H-tetrazoles are also potent in the activation of phosphoramidites; these activators have been particularly useful in RNA synthesis (Wincott et al, 1995;Wu and Pitsch, 1998).…”

Synthetic and conformational studies of branched and lariat RNAs. Modelling the lariat formed in the splicing reaction — A critical review

“…One important criteria that has to be fulfilled in order for the next step to be successful protecting group. Results from previous investigations on phosphate migration in the ribonucleoside 2',Y-cis-diol system have shown that the Y--,5'-phosphodiester linkage in such a system migrates only to a negligible degree under mild acidic conditions (80~o aqueous acetic acid) (Kwiatkowski and Chattopadhyaya 1982) or 0"01 M aqueous HC1 (Griffin et al 1968;Kwiatkowski and Chattopadhyaya 1982) during 6 h at 20~ Also under neutral conditions (TBAF trihydrate in THF 12-24 h, 20~ the phosphodiester linkage is reasonably stable (Scaringe et (Huss et al 1988a;Vial et al 1988), O-alkyl-bis-(1,2,4-triazolo) phosphite (Fourrey and Varenne 1984;Fourrey et a/ 1987), O-alkyl-N,N-dialkylmonochlorophosphines (Zhou et al 1987), nucleoside-5'-phosphoramidites (Kierzek et al 1986) and 5'-H-phosphonates F61desi et a/ 1989). Phosphoro-bis-anilidate (Sekine and Hata 1985;Sekine et al 1987) and methylphosphotriester (Fourrey et al 1987) functions have also been employed under stringently controlled conditions, but these are not versatile because of their inherent susceptibility to migrate to the vicinal hydroxyl group.…”

“…Results from previous investigations on phosphate migration in the ribonucleoside 2',Y-cis-diol system have shown that the Y--,5'-phosphodiester linkage in such a system migrates only to a negligible degree under mild acidic conditions (80~o aqueous acetic acid) (Kwiatkowski and Chattopadhyaya 1982) or 0"01 M aqueous HC1 (Griffin et al 1968;Kwiatkowski and Chattopadhyaya 1982) during 6 h at 20~ Also under neutral conditions (TBAF trihydrate in THF 12-24 h, 20~ the phosphodiester linkage is reasonably stable (Scaringe et (Huss et al 1988a;Vial et al 1988), O-alkyl-bis-(1,2,4-triazolo) phosphite (Fourrey and Varenne 1984;Fourrey et a/ 1987), O-alkyl-N,N-dialkylmonochlorophosphines (Zhou et al 1987), nucleoside-5'-phosphoramidites (Kierzek et al 1986) and 5'-H-phosphonates F61desi et a/ 1989). Phosphoro-bis-anilidate (Sekine and Hata 1985;Sekine et al 1987) and methylphosphotriester (Fourrey et al 1987) functions have also been employed under stringently controlled conditions, but these are not versatile because of their inherent susceptibility to migrate to the vicinal hydroxyl group. Various 3'-0-or 2'-O-protectors (R 2 in G and R2 in N) such as t-butyldimethylsilyl (Kierzek et al 1986: Fourrey et al 1987) l,l,3,3-tetraisopropyl-l,3-disiloxane-3-yl (Zhou et a11987, 1988, 4-methoxytetrahydropyranyl (Huss et al 1988a) and pixyl (Balgobin et al 1988;Vial et al 1988;Frldesi et al 1989) groups have been shown to fulfil the requirements of removal under mild conditions without causing any migration of the vicinal phosphodiester linkage, thus allowing regiospecific introduction of the second phosphate function at the branch-point [H~l(path:i) and O ~ P(path:n)].…”