The 2-(N-Formyl-N-methyl)aminoethyl Group as a Potential Phosphate/Thiophosphate Protecting Group in Solid-Phase Oligodeoxyribonucleotide Synthesis

Abstract

[reaction in text] The 2-(N-formyl-N-methyl)aminoethyl deoxyribonucleoside phosphoramidite 1 has been synthesized and used in the solid-phase synthesis of an octadecathymidylic acid as a cost-efficient monomer for potential application in the preparation of therapeutic oligonucleotides. The 2-(N-formyl-N-methyl)aminoethyl group can be cleaved from oligonucleotides according to a unique thermolytic cyclodeesterification process at pH 7.0. In addition to being cost-effective, the use of 1 simplifies oligonucleotide postsynthesis processing by eliminating the utilization of concentrated ammonium hydroxide in oligonucleotide deprotection.

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs

“…The chromatographic profile of CpG ODN fma 1555 is shown in Figure 1 and exhibits a retention time ( t R ) of 37 min. The shape of the peak corresponding to the purified oligonucleotide is consistent with that of a complex mixture of rotameric diastereomers (2). …”

“…This compound (Scheme 2) was prepared from the reaction of 2-(methylamino)ethanol (Aldrich) with ethyl formate (Aldrich) as described earlier (2). …”

“…This phosphinylating reagent (Scheme 2) was prepared following a procedure that had been modified from its earlier version (2,12). To a stirred solution of 2-( N -formyl- N -methyl)aminoethan-1-ol (3.50 g, 34.0 mmol) and N ,  N -diisopropylethylamine (35.0 ml, 201 mmol) in anhydrous dichloromethane (20 ml) was added, at 25°C, a solution of bis ( N , N -diisopropylamino)chlorophosphine (Aldrich) (9.98 g, 37.4 mmol) in dry dichloromethane (10 ml).…”

“…Over the last few years, our research efforts have focused on the design and development of thermolytic groups for 5′-hydroxyl (1) and phosphate (2–7) protection in an attempt to implement a ‘heat-driven’ process (8) for the synthesis of DNA oligonucleotides on microarrays. In sharp contrast to the current methods employed for oligonucleotide synthesis, such a process would involve rapid and efficient thermal removal of protecting groups from oligonucleotides under neutral conditions throughout chain assembly and final deprotection.…”

Strategies Useful for the Chemical Synthesis of Oligonucleotides and Related Compounds

“…In order to eliminate possible sidereactions caused by the presence of pyrrolidine, Beaucage and coworkers later developed MTFAB, which releases less nucleophilic N-methypyrrolidine as a coproduct [41,43]. The utility of the 2-(N-formyl-N-methyl)aminoethyl group for the solid-phase synthesis has also been investigated [44]. This group can be cleaved not only by gaseous ammonia, but is also cleaved by buffer solution at pH 7.0 (3 h at 90 °C).…”