title: Chemical stability of 2'-deoxy-5-methylisocytidine during oligodeoxynucleotide synthesis and deprotection.
abstract: Previous studies have encountered difficulties with degradation of some isocytidine derivatives during solid-phase synthesis and deprotection of oligonucleotides. Here we investigate the degradation of a commonly used derivative, 2'-deoxy-5-methylisocytidine, during oligodeoxynucleotide synthesis and deprotection. A small, but detectable amount of hydrolytic deamination occurred at ca. 0.5% of 2'-deoxy-5-methylisocytidine residues using routine synthesis and deprotection conditions. Depyrimidination, or cleavage of the glycosylic bond, occurred to a far lesser extent during alkaline deprotection than previously suggested. In contrast to model studies of nucleoside monomers, significant depyrimidination was not observed, even at extended incubation times.
authors.affiliation: Nucleic Acid Diagnostics, Bayer Diagnostics, Emeryville, CA 94608, USA.
authors.forename: Chenxia
authors.initials: C
authors.lastname: Wang
authors.forename: Jialiang
authors.initials: J
authors.lastname: Jiang
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Battersby
mesh_terms: D000241:Adenosine; D020029:Base Pairing; D001483:Base Sequence; D003562:Cytidine / Q000031:analogs & derivatives* / Q000737:chemistry*; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D003641:Deamination; D019075:Electrophoresis, Capillary; D024202:Electrophoretic Mobility Shift Assay; D006151:Guanosine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis*; D011741:Pyrimidine Nucleosides / Q000737:chemistry; D013997:Time Factors
chemical_list: C413872:2'-deoxy-5-methylisocytidine; D009838:Oligodeoxyribonucleotides; D011741:Pyrimidine Nucleosides; C093270:isocytosine; D006151:Guanosine; C008184:isoguanosine; D003562:Cytidine; D003596:Cytosine; D000241:Adenosine