Synthesis of Acyclic Nitroazole Nucleosides and Their Incorporation into Oligonucleotides, and Their Duplex and Triplex Formation

Abstract

Acyclic nucleosides of 4-nitro-1H-imidazole and 4-nitropyrazole have been synthesized by nucleophilic addition of the appropriate 4-nitroazole to (À)-(S)-(hydroxymethyl)oxirane in the presence of a catalytic amount of potassium carbonate. ()-(R)-3-(4-nitro-1H-imidazol-1-yl)propane-1,2-diol and ()-(R)-3-(2-methyl-4-nitro-1H-imidazol-1-yl)propane-1,2-diol were also obtained in an independent reaction starting from appropriate 1,4-dinitro-1H-imidazole and ()-(R)-3-aminopropane-1,2-diol. ()-(R)-3-(4-Nitropyrazol-1-yl)-propane-1,2-diol was also obtained by direct noncatalyzed addition of 4-nitropyrazole to (À)-(S)-(hydroxymethyl)oxirane, whereas the (S)-enantiomer was obtained by reaction of 4-nitropyrazole with ()-(S)-1,2-Oisopropylideneglycerol under Mitsunobu reaction conditions, followed by a cleavage of the isopropylidene group with 80% AcOH. Racemization during any of these syntheses has not been observed. 3-(4-Nitroazol-1-yl)propane-1,2-diols were incorporated into a 26-mer oligonucleotide. UV Thermal melting studies of duplexes of the oligonucleotides with 4-nitropyrazole or 4-nitro-1H-imidazole paired with four natural bases showed moderately decreased stabilities of the duplexes. A narrow range of melting temperatures, typically being within 28 for each acyclic nucleoside, fulfill one of the requirements of using acyclic 4-nitroazoles as general bases. Single incorporation of 4-nitroazoles into a 14-mer triplex forming oligonucleotide resulted in considerably decreased triplex stabilities.

Universal Base Analogues and their Applications to Biotechnology

“…These authors found that all the modified bases led to destabilized triplexes, and confirmed the report that 3-nitropyrrole (1) destabilized triplex formation [79][80][81]. Similar data were observed for the stability of acyclic nitroazole nucleosides in triplexes [82]. However, further studies showed that stable triplexes containing 1 in the third strand can be obtained in the presence of benzopyridoindole.…”

1,4-Dinitro-1H-imidazoles

“…73 Experience gathered in the application of the ANRORC reaction in syntheses of nucleosides was expanded by Walczak et al to acyclic nucleosides. 74 The ANRORC reaction of compounds 1 and 2 was applied for conversion of unprotected 2-amino-2-deoxy-D-hexopyranoses into 2-deoxy-2-(4′-nitro-1′H-imidazol-1′-yl)-D-hexopyranoses. The obtained mixtures of anomers were separated into pure products following acetylation.…”

Universal base analogues and their applications in DNA sequencing technology

“…7) into oligonucleotides. 60 Thermal melting studies of duplexes of the oligonucleotides with 4-nitropyrazole or 4-nitro-1H-imidazole paired with four natural bases showed that the acyclic 4-nitro-1H-imidazole (R) gave a range of 4 uC, while the 2-methyl-4-nitro-1H-imidazole (R), 4-nitro-1H-pyrazole (R) and 4-nitro-1H-pyrazole (S) each gave a very narrow range of 2 uC. The duplexes from oligonucleotides with the sugar 3-nitropyrrole in the middle of a T region were reported to melt by 11-14 uC lower than the corresponding sequences containing an A?T base pair, whereas for the 26-mer only a 5-10 uC lower melting temperature was observed for all the investigated acyclic azoles in a T region when compared with the A?T base pair.…”