Synthesis of Endcap Dimethoxytrityl Phosphoramidites for Endcapped Oligonucleotides

Abstract

Endcaps may be either aromatic or aliphatic molecules that specifically crossâ link the 5â ² end of one strand with the 3â ² end of the complementary strand in a DNA duplex. Endcaps may be viewed as a replacement of the loop region nucleotides of a DNA hairpin, with the added advantage of increased thermal stability. An endcap is incorporated into the sequence during oligonucleotide synthesis. Three endcaps are described in this unit. The naphthalene diimide endcap prefers to base stack with GC base pairs. The terthiophene endcap has higher lipophilicity than the naphthalene diimide endcap and provides higher stability when stacked over an AT base pair. The 2,2â ²â oxydiacetamide endcap provides lower enhancement in stability but a more rigid and wellâ defined structure than the oligo(ethylene glycol) endcaps. Synthesis of endcapped oligonucleotides can be carried out using standard automated synthesis protocols with only minor modifications.