Synthesis of 2‘-O-[2-[(N,N-Dimethylamino)oxy]ethyl] Modified Nucleosides and Oligonucleotides

• Published in: Journal of organic chemistry Vol. 67; no. 2; pp. 357 - 369
• Main Authors: Prakash, Thazha P, Kawasaki, Andrew M, Fraser, Allister S, Vasquez, Guillermo, Manoharan, Muthiah
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 25.01.2002; Amer Chemical Soc
• Subjects: Animals; Base Sequence; Carbohydrates. Nucleosides and nucleotides; Catalysis; Chemistry; Chemistry, Organic; Chemistry, Organic - methods; Chromatography, High Pressure Liquid; DNA, Complementary - chemistry; Exact sciences and technology; Mass Spectrometry; Molecular Conformation; Molecular Sequence Data; Molecular Structure; Nucleic Acid Hybridization; Nucleosides, nucleotides and oligonucleotides; Oligonucleotides, Antisense - chemical synthesis; Oligonucleotides, Antisense - chemistry; Oligonucleotides, Antisense - metabolism; Organic chemistry; Oxidation-Reduction; Phosphodiesterase I; Phosphoric Diester Hydrolases - metabolism; Physical Sciences; Preparations and properties; Purine Nucleosides - chemical synthesis; Purine Nucleosides - chemistry; Purine Nucleosides - metabolism; Pyrimidine Nucleosides - chemical synthesis; Pyrimidine Nucleosides - chemistry; Pyrimidine Nucleosides - metabolism; RNA, Complementary - chemistry; Science & Technology; Snake Venoms - enzymology; Substrate Specificity; FUNCTIONALIZATION; OXIDATION; PROTECTION; STABILITY; ANTISENSE; ADENOSINE; EXONUCLEASE RESISTANCE; HYBRIDIZATION; GUANOSINE; 2-AMINOADENOSINE; Purine nucleotide; Purine nucleoside; Regioselectivity; Chemical stability; Mitsunobu reaction; Organic phosphoramidite; Thermal denaturation; Complementary RNA; Hybridization; Antisense oligonucleotide; Chemical modification; Functionalization; Oligonucleotide; Solid phase; Chemical synthesis; Pyrimidine nucleoside; Pyrimidine nucleotide; Organic hydroxylamine
• ISSN: 0022-3263; 1520-6904
• DOI: 10.1021/jo0103975

A versatile synthetic route has been developed for the synthesis of 2‘-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2‘-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2‘-O-DMAOE purine nucleosides, the key intermediate B (Scheme ) was obtained from the 2‘-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon−carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2‘-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2‘-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2‘-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2‘-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2‘-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3‘-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2‘-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t 1/2 > 24 h.