Nucleotides, Part LXVII, The 2-Cyanoethyl and (2-Cyanoethoxy)carbonyl Group for Base Protection in Nucleoside and Nucleotide Chemistry

Abstract

The amino functions of the common 2'-deoxyribo-and ribonucleosides were blocked by the (2-cyanoethoxy)carbonyl group on treatment with 2-cyanoethyl carbonochloridate (5) or 1-[(2-cyanoethoxy)carbonyl]-3-methyl-1H-imidazolium chloride (6) leading to 7, 18, 8, 19, 9, and 20. In 2'-deoxyguanosine, the amide group was additionally blocked at the O 6 position by the 2-cyanoethyl ( 3 27) and 2-(4-nitrophenyl)ethyl group ( 3 31, 32). Comparative kinetic studies regarding the cleavage of the ce/ceoc and npe/npeoc group by b-elimination revealed valuable information about the ease and sequential deprotection of the various blocking groups at different sites of the nucleobases. Besides the 5'guanosine analog 40 is recommended as building block for oligo-2'-deoxyribonucleotide synthesis. Introduction. ± The development of the 2-(4-nitrophenyl)ethyl (npe) and [2-(4-nitrophenyl)ethoxy]carbonyl (npeoc) groups as versatile protective groups for nucleobases [2], phosphate [3] [4], and phosphite functions [5] [6] broadened the strategy of nucleoside and nucleotide protection in oligonucleotide synthesis universally. The great advantange of these groups is their high stability under acidic and mild basic hydrolytic conditions as, for example, in the presence of ammonia and amines in MeOH, dioxane, or H 2 O, whereas their cleavage can easily and quantitatively be achieved by 1,8-diazabicyclo[5.4.0]undecene (DBU) in aprotic solvents by a b-elimination process.The 2-cyanoethyl (ce) group [7] [8] is the most common blocking group for the phosphate and phosphite moiety of nucleotides, but strangely enough, the ce and its corresponding (2-cyanoethoxy)carbonyl (ceoc) group have not been applied for base protection in analogy to the npe/npeoc couple. Several years ago, we [9] [10] developed the ce/ceoc strategy as an alternative approach for the synthesis of special oligonucleotides. Details about the nucleobase protection by the ce and ceoc group will now be reported since N-{[(2-cyanoethoxy)carbonyl]oxy}succinimide has recently been described as a new reagent for protection of amino groups in oligonucleotides [11]. We protected the amino group in cytidine, adenosine, and guanosine as well as in the corresponding 2'-deoxynucleosides with the ceoc group and utilized the ce group

Site-Specific Synthesis of N4-Acetylcytidine in RNA Reveals Physiological Duplex Stabilization

“…To address the first criterion, we were inspired by prior syntheses of Oacetylated RNAs, which like ac4C are sensitive to nucleophilic cleavage. 22,23 These studies employed Ncyanoethyl O-carbamate (N-ceoc) 24 nucleobases that could be deprotected using the non-nucleophilic base 1,5-diazabicyclo(4.3.0)non-5-ene (DBU). To determine the orthogonality of N-ceoc protection and N 4acetylation, we analyzed the compatibility of DBU and ac4C using a series of simple model substrates (Figure 2b).…”

Nucleobase Protection of Deoxyribo‐ and Ribonucleosides

“…The 2cyanoethyl (ce) group is the most common phosphate-protecting group in oligonucleotides; however, the ce and corresponding 2-(cyano-ethoxycarbonyl) (ceoc) groups were not utilized for nucleobase protection until 2000. Merk, Reiner, Kvasuk, & Pfleiderer (2000) developed ceoc protection for the protection of the exocylic amino group of adenine, guaninine, and cytosine. The (2-cyanoethoxy)carbonylation reactions of nucleosides were carried out with either 2-cyanoethyl carbonochloridate 30b or 1-((2-cyano-ethoxy)carbonyl)-3-methyl-1 Himidazolium chloride 30c (Fig.…”

“…The (2-cyanoethoxy)carbonylation reactions of nucleosides were carried out with either 2-cyanoethyl carbonochloridate 30b or 1-((2-cyano-ethoxy)carbonyl)-3-methyl-1 Himidazolium chloride 30c (Fig. 2.1.17), which were synthesized by the modified procedures of Merk et al (2000) and Wiesler & Caruthers (1996), affording the ceoc-protected nucleosides 31a-c (Fig. 2.1.18).…”

Nucleobase Protection of Deoxyribo‐ and Ribonucleosides

“…The 2‐cyanoethyl (ce) group is the most common phosphate‐protecting group in oligonucleotides; however, the ce and corresponding 2‐(cyano‐ethoxycarbonyl) (ceoc) groups were not utilized for nucleobase protection until 2000. Merk, Reiner, Kvasuk, & Pfleiderer () developed ceoc protection for the protection of the exocylic amino group of adenine, guaninine, and cytosine. The (2‐cyanoethoxy)carbonylation reactions of nucleosides were carried out with either 2‐cyanoethyl carbonochloridate 30b or 1‐((2‐cyano‐ethoxy)carbonyl)‐3‐methyl‐1 H ‐imidazolium chloride 30c (Fig.…”

“…The (2‐cyanoethoxy)carbonylation reactions of nucleosides were carried out with either 2‐cyanoethyl carbonochloridate 30b or 1‐((2‐cyano‐ethoxy)carbonyl)‐3‐methyl‐1 H ‐imidazolium chloride 30c (Fig. ), which were synthesized by the modified procedures of Merk et al () and Wiesler & Caruthers (), affording the ceoc‐protected nucleosides 31a‐c (Fig. ).…”