A Method for Solid-Phase Synthesis of Oligonucleotide 5‘-Peptide-Conjugates Using Acid-Labile α-Amino Protections Simone Zaramella Esther Yeheskiely Roger Strömberg 10.1021/ja046945o.s001 https://acs.figshare.com/articles/journal_contribution/A_Method_for_Solid_Phase_Synthesis_of_Oligonucleotide_5_Peptide_Conjugates_Using_Acid_Labile_Amino_Protections/3317812 We describe the development of a solid-phase technique for the synthesis of 5‘-peptide−oligonucleotide conjugates (POCs) with a uniform protection strategy for the nucleic acid and the peptide fragments. On the α-amino function, the amino acid building blocks were protected with the 2-(biphenyl-4-yl)propan-2-yloxycarbonyl (Bpoc) group. This protection is removed during the stepwise peptide elongation by the same acidic conditions used for removal of the dimethoxytrityl (DMT) group used in the oligonucleotide assembly (3% trichloroacetic acid, 2 min). The 2-(3,5-dimethoxyphenyl)propan-2-yloxycarbonyl (Ddz) group was also tested. With this somewhat more stable group, a prolonged contact with the acid (at least 16 min) was required for accomplishing complete α-amino deprotection, which resulted in some degree of depurination of the acid-sensitive DNA chain. Base-labile acyl protections were adopted for the side-chains of histidine, lysine, and the nucleobase amino functions. These were all removed in the final deblocking step by ammonolysis. This uniform protection scheme for the peptide and the oligonucleotide enabled the total stepwise synthesis of model conjugates in the 3‘ → <i>N</i> direction with high efficiency and purity. 2004-11-03 00:00:00 peptide fragments acidic conditions uniform protection strategy DMT peptide elongation oligonucleotide uniform protection scheme 2 min function DNA acid building blocks synthesis deblocking step model conjugates POC 16 min