Synthesis of (2′S)‐ and (2′R)‐2′‐Deoxy‐2′‐[(2‐methoxyethoxy)amino] Pyrimidine Nucleosides and Oligonucleotides

Abstract

Syntheses of specified 2'-modified nucleosides were achieved: a) via oximation of the 5',3'-blocked 2'-oxocytidine, followed by reduction, or b) by intramolecular nucleophilic addition of 3'-(2-methoxyethoxy)carbamate to the 2'-position with opening of O(2),2'-anhydrouridine. For the first time, 3'-phosphoroamidites of these 2'-modified nucleosides were successfully incorporated into oligonucleotides by solid-phase synthesis. Incorporation of 2'-modified nucleotides into oligodeoxyribonucleotides had a negative effect on the duplex T(m) values with the DNA or RNA complements. Nevertheless, modified nucleotides have shown good target recognition; the (S)-isomer binds preferably to RNA and the (R)-isomer to DNA. Both modified nucleosides significantly increased nuclease resistance of the oligodeoxyribonucleotides.

Mass Determination of Phosphoramidites

“…Because of the relatively large mass determination errors obtained from MALDI-TOF-MS analyses, the method has limitations in the determination of molecular composition (Korshun et al, 2002;Ashraf et al, 2003;Mckeen et al, 2003;Zhu and Schmidt, 2003;Kirk and Bohn, 2004;Lu et al, 2004;Zatsepin et al, 2004). The low-resolution LSIMS spectrum of S.1a using the TEOA/NaCl matrix (Fig.…”

“…Since determination of molecular composition requires mass errors of less than ±3 ppm, MALDI‐TOF‐MS cannot give the molecular composition of S.1a . Because of the relatively large mass determination errors obtained from MALDI‐TOF‐MS analyses, the method has limitations in the determination of molecular composition (Korshun et al, ; Ashraf et al, ; Mckeen et al, ; Zhu and Schmidt, ; Kirk and Bohn, ; Lu et al, ; Zatsepin et al, ). The low‐resolution LSIMS spectrum of S.1a using the TEOA/NaCl matrix (Fig.…”