Oligonucleotides Containing 7-Deaza-2′-deoxyxanthosine: Synthesis, Base Protection, and Base-Pair Stability

Oligonucleotides incorporating 7-deaza-2′-deoxyxanthosine (3) and 2′-deoxyxanthosine (1) were prepared by solid-phase synthesis using the phosphoramidites 6–9 and 16 which were protected with allyl, diphenylcarbamoyl, or 2-(4-nitrophenyl)ethyl groups. Among the various groups, only the 2-(4-nitrophenyl)ethyl group was applicable to 7-deazaxanthine protection being removed with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) by β-elimination, while the deprotection of the allyl residue with Pd0 catalyst or the diphenylcarbamoyl group with ammonia failed. Contrarily, the allyl group was found to be an excellent protecting group for 2′-deoxyxanthosine (1). The base pairing of nucleoside 3 with the four canonical DNA constituents as well as with 3-bromo-1-(2-deoxy-β-D-erythro-pentofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine (4) within the 12-mer duplexes was studied, showing that 7-deaza-2′-deoxyxanthosine (3) has the same universal base-pairing properties as 2′-deoxyxanthosine (1). Contrary to the latter, it is extremely stable at the N-glycosylic bond, while compound 1 is easily hydrolyzed under slightly acidic conditions. Due to the pKa values 5.7 (1) and 6.7 (3), both compounds form monoanions under neutral conditions (95% for 1; 65% for 3). Although both compounds form monoanions at pH 7.0, pH-dependent Tm measurements showed that the base-pair stability of 7-deaza-2′-deoxyxanthosine (3) with dT is pH-independent. This indicates that the 2-oxo group is not involved in base-pair formation.