Synthesis of oligonucleotides containing bulky adducts at guanine N2 via the phosphoramidite of O2-triflate-O6-NPE 2′-deoxyxanthosine (original) (raw)
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Chemical research …, 1996
Improved methodology has been developed for preparation of oligodeoxynucleotides bearing adducts on the N 2 position of guanine in which the adduction reaction is carried out in homogeneous solution rather than while the oligonucleotide is immobilized on a solid matrix. The methodology utilizes a new synthon, 2-fluoro-O 6-(trimethylsilylethyl)-2′-deoxyinosine (3). Nucleoside 3 is stable to the conditions of oligonucleotide synthesis, but the O 6 protection is eliminated under very mild conditions following displacement of the 2-fluoro group by amine nucleophiles. Oligonucleotides containing 3 could be removed from the solid support by treatment with 0.1 M NaOH (8 h, rt) without disruption of 3. Reaction of the crude, partially deprotected oligonucleotide with (R)-2-amino-2-phenylethanol in homogeneous solution, followed by removal of the remaining protective groups with NH 4 OH (60°C, 8 h) and then 0.1% acetic acid, gave the adducted oligonucleotide in good purity and yield. Alternatively, fully deprotected oligonucleotide containing 3 could be prepared by use of labile phenoxyacetyl-type protecting groups on the exocyclic amino groups.
Nucleic Acids Research, 1986
Phosphoramidite reagents can phosphitylate guanine bases at the O-position during solid phase synthesis and serious chain cleavage occurs if the base phosphitylation is not eliminated before the iodine/water oxidation step. This can be accomplished by i) blocking the O^-position with a 2-cyanoethyl protecting group for deoxyribonucleotides or with a p-nitrophenylethyl group for ribonucleotides, ii) regenerating the guanine base with water or acetate ions, or iii) using N-methylanilinium trifluoroacetate (TAMA) as the phosphoramidite activator. The effectiveness of these methods was demonstrated by both 3 1 P NMR studies and by the synthesis of d(Gp) 2 3G, (Gp) 14 G, and d-(Gp) 1 3rG sequences.
Nucleos Nucleot Nucleic Acids, 1997
4'-C-(Hydroxymethyl)thymidine derivative 1 was transformed into phosphoramidite 7 which was used for incorporation of 4'-C-hydroxymethyl funetionalized thymidine monomers once and twice into 17-mer oligodeoxynucleotides (ODNs). The novel modified ODNs exhibited excellent affinity towards complementary DNA and increased resistance towards 3'-exonucleolytie degradation compared to unmodified ODNs. Ideal antisense molecules for regulation of gene expression need e.g. to interact with high specificity and affinity with target nucleic acid and to exhibit stability towards degradative nucleases. Therefore, a variety of chemically modified ODNs have been synthesized and characterized in the last years. 1,2 Recently, Maag et al. 3 have incorporated thymidine monomers containing a 4'-C-linker arm terminating in a biotin functionality into ODNs for detection of specific DNA sequences. It was found that one and two 4'-C-modifications result in quite small decreases in melting temperature (-1.5 °C / modification). 3 Independently, as part of our
Chemical Research in Toxicology, 2006
Synthesis of 2′-deoxyguanosine-C8 adducts (dG-C8 adducts) with mutagenic/carcinogenic heterocyclic amines (HCAs) was achieved via the Buchwald-Hartwig arylamination reaction. By using tris-(dibenzylideneacetone)dipalladium (Pd 2 dba 3) and 9,9-dimethyl-4,5-bis(diphenylphosphino)xanthene (xantphos) with a cesium carbonate (Cs 2 CO 3) base at a reaction temperature of 100∼120°C, we obtained derivatives of dG-C8 adducts with 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), 2-amino-6-methyldipyrido[1,2-a:3′,2′-d]imidazole (Glu-P-1), 3-amino-1,4-dimethyl-5H-pyrido[4,3-b]indole (Trp-P-1), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), and 2-amino-1-methyl-6-phenylimidazo[4,5b]pyridine (PhIP) in 69%∼97% yield from the cross-coupling of an 8-bromodeoxyguanosine derivative. In the case of PhIP, it was found that dimethyl sulfoxide (DMSO) was the critical solvent for the arylamination reaction. Subsequent deprotection of the resulting dG-C8 adduct derivatives yielded authentic samples of dG-C8 adducts with HCAs. The dG-C8-PhIP adduct was further converted into a suitably protected phosphoramidite derivative for automated DNA synthesis. Synthesis of oligonucleotides wherein PhIP adducted on each G within a triple G sequence in codon 869 (TCC GGG AAC) of rat Apc genes was performed with a modification in the coupling time and deprotection procedures.
Synthesis of oligodeoxynucleotides containing 6-N-([13C]methyl)adenine and 2-N-([13C]methyl)guanine
J Chem Soc Perkin Trans 1, 1997
Oligonucleotides containing 6-N-([ 13 C]methyl)adenine and 2-N-([ 13 C]methyl)guanine have been prepared for NMR studies using the deprotection step to introduce the [ 13 C]methylamine group. For this purpose, the use of 2'-deoxy-6-O-(pentafluorophenyl)inosine 1 and 2'deoxy-2-fluoro-6-O-[2-(4-nitrophenyl)-ethyl]inosine 2 as precursors of the N-methylated nucleosides is described. Preliminary NMR characterization of the 13 C-labelled oligonucleotides shows that the 13 C chemical shift of the methyl group in N-methylguanine is sensitive to duplex formation, making it a useful local probe.
Tetrahedron, 2006
A general and convenient method for synthesis of modified oligonucleotides by use of new non-nucleoside phosphoramidites is reported. A chiral 1,3-diol backbone of the modifying reagents is generated either from (R)-(+)-a-hydroxy-g-butyrolactone or (R)-(À)pantolactone. Aliphatic amines were acylated with the lactones to give the corresponding N-substituted 2,4-dihydroxybutyramides. After protection of a side chain, if necessary, the diols were converted into phosphoramidites or solid supports suitable for use in oligonucleotide synthesis. The reagents allow single, multiple or combined introduction of various functions (e.g., alkylamine, imidazole and pyrene residues) into synthetic oligonucleotides. The structures of the conjugates were confirmed by MALDI-TOF mass spectrometry.