Labile exocyclic amine protection of nucleosides in DNA, RNA and oligonucleotide analog synthesis facililating N-deacylation, minimizing depurination and chain degradation

Synthesis and Properties of Oligonucleotides Containing 8-Bromo-2′-Deoxyguanosine

“…and F (5' 5G5GCGCGCG 3') where B= 8-bromoguanine and 5= 5-bromocytosine were prepared on a DNA synthesizer using both standard (benzoyl-dA and dC and isobutyryl-dG) and t-butylphenoxyacetyl (TBPA)-protected 19 2-cyanoethyl phosphoramidites together with phosphoramidite 4 and the commercially available phosphoramidite of 5-bromo-2'-deoxycytidine (protected with the benzoyl group) and the appropriate succinyl-CPG supports. During the syntheses, 0.02 M iodine solution (tetrahydrofurane: water: pyridine 7:1:2) was used to prevent the formation of N-cyano nucleosides.…”

“…20 t-Butylphenoxyacetyl anhydride was used instead of acetic anhydride in the syntheses with TBPA-protected phosphoramidites to prevent acetylation of TBPAprotected bases. 19 After the assembly of the sequences, oligonucleotide-supports were treated with concentrated (30%) aqueous ammonia solution. The time needed for the removal of the dmf group on the dimer A was found to be less than 1 hour at room temperature, because a single peak was observed on reverse phase HPLC that had the expected molecular weight and the expected nucleoside composition after enzymatic digestion.…”

“…Oligonucleotides were prepared on an automatic DNA synthesizer using commercially available 2-cyanoethyl phosphoramidites and the modified phosphoramidite. Oligonucleotide sequences B and C were prepared using using both standard (benzoyl-dA and dC and isobutyryl-dG) and t-butylphenoxyacetyl (TBPA)-protected 19 phosphoramidites. Oligonucleotide sequences E and F were prepared using using t-butylphenoxyacetyl (TBPA)-protected phosphoramidites as decribed.…”

Matrix-assisted laser desorption/ionization mass spectrometry of immobilized duplex DNA probes

“…A 55 base deoxynucleotide (5'-AGC TAG TCA TGT AAT GCA GGT CCT ACA GTC AAT GGC CGT AAT GAC CGT TAT TTF1l T-3') was synthesized on 13.8 mg CPG in situ using P-cyanoethyl phosphoamidite chemistry (18,19), a DNA synthesizer (MilliGen Model 7500) and the more base-labile 4-t-butylphenoxyacetyl group for protection of the exocyclic amino group (20,21). Deprotection of the amino and phosphate protecting groups was accomplished by a 2 h treatment with methanol saturated with ammonia at room temperature.…”

An Efficient One-pot N-Acylation of Deoxy- and Ribo-cytidine Using Carboxylic Acids Activated in situ with 2-Chloro-4,6-dimethoxy-1,3,5-triazine

“…To our knowledge, no general method has been reported previously that is single-step and useful for all protecting groups, such as acetyl, benzoyl, and phenoxyacetyl, in which the protecting group have been installed on the base moiety of cytidine and 2'-deoxycytidine without prior O-protection and in the absence of a catalyst. Additionally, present methodology may be extended to a variety of selective N-acylation of cytidine using other carboxylic acids such as t-butylphenoxyacetyl (t-BPA), 21 isopropyl-phenoxyacetyl (IPAC), and isopropoxyacetyl (IPOAC) 5 to achieve milder and faster deprotection in the oligonucleotides synthesis.…”