Synthesis of antisense oligonucleotides with minimum depurination.
The removal of 4,4'-dimethoxytrityl (DMTr) groups from oligonucleotides at low pH and the acid lability of the glycosidic linkage of purine nucleotides constitute an inherent conflict in preparative oligonucleotide chemistry. The use of a mildly acidic NaOAc buffer (10 mM, pH 3.0-3.2) allows adjustment of the pH in a range where the progress of the DMTr removal reaction can be monitored conveniently by HPLC and the optimum reaction time can be calculated. As a result, oligonucleotides with minimum depurination are obtained.
Isis Pharmaceuticals, Inc., Carlsbad, California 92008, USA. akrotz@isisph.com
Achim H
AH
Krotz
Douglas L
DL
Cole
Vasulinga T
VT
Ravikumar
D000225:Adenine / Q000032:analysis; D002851:Chromatography, High Pressure Liquid; D006147:Guanine / Q000032:analysis; D006863:Hydrogen-Ion Concentration; D008956:Models, Chemical; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D016376:Oligonucleotides, Antisense / Q000138:chemical synthesis* / Q000737:chemistry; D011687:Purines / Q000737:chemistry; D014320:Triphenylmethyl Compounds / Q000737:chemistry
D009838:Oligodeoxyribonucleotides; D016376:Oligonucleotides, Antisense; D011687:Purines; D014320:Triphenylmethyl Compounds; D006147:Guanine; C060949:4,4'-dimethoxytrityl cation; D000225:Adenine