title: Conversion of adenine to 5-amino-4-pyrimidinylimidazole caused by acetyl capping during solid phase oligonucleotide synthesis.
abstract: The acetyl capping reaction used throughout solid phase oligonucleotide synthesis is meant to minimize n-1 deletionmer impurities by terminating sequences that fail to couple to a phosphoramidite. However, the reaction is also responsible for the formation of a number of impurities. One capping-related impurity has an additional mass of 98amu from the parent oligonucleotide. The n+98 amu impurity was found to result from modification of an adenine nucleobase. The structure of the impurity was determined by preparation of an oligonucleotide enriched in n+98 amu, enzymatic digestion to individual nucleosides, isolation of the pure nucleoside+98 amu species, crystallization, and X-ray crystallographic analysis. The n+98 amu impurity is an oligonucleotide in which one adenine residue has been converted to 5-amino-4-pyrimidinylimidazole. The mechanism of formation of the impurity was investigated, and a mechanism is proposed.
authors.affiliation: Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, USA. Electronic address: arodrigu@ionisph.com.
authors.forename: Andrew A
authors.initials: AA
authors.lastname: Rodriguez
authors.affiliation: Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, USA.
authors.forename: Isaiah
authors.initials: I
authors.lastname: Cedillo
authors.affiliation: Ionis Pharmaceuticals, Inc., 2855 Gazelle Ct., Carlsbad, CA 92010, USA.
authors.forename: Andrew K
authors.initials: AK
authors.lastname: McPherson
mesh_terms: D000225:Adenine / Q000737:chemistry*; D007093:Imidazoles / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry
chemical_list: C000621215:5-amino-4-pyrimidinylimidazole; D007093:Imidazoles; D009841:Oligonucleotides; D000225:Adenine
keywords: Acetyl; Adenine; Adenosine; Capping; Impurity; Modification; Oligonucleotide; Solid-phase