Two 5 modified 2'-deoxyuridin triphosphates and a 7 modified 2'-deoxy-7-deazaadenosine were synthesized carrying a terminal azide linked to the base. For probing the sterical influence on incorporation and Staudinger ligation different sized flexible linkers were chosen. All three nucleotides can completely replace their natural counterparts in primer extension as well as polymerase chain reactions (PCR) using Pwo DNA polymerase. For azide labeled primer extension products subsequent conjugation of suitably functionalized phosphines via Staudinger ligation was achieved, e.g. for the conjugation of biotin as an affinity tag.