A new synthetic protocol for labeled oligonucleotides, using a chemically cleavable universal linker

A two-step general method for labeling of synthetic oligonucleotides is described. The protocol employs a cleavable universal linker, 5′-O-(4,4′-dimethoxytrityl)-3′-O-benzoyl-2′-O-(2-cyanoethyl-N,N-diisopropyl)-uridine phosphoramidite, to effect coupling to polymer-bound oligonucleotide chains. Sequentially, coupling with commercially available phosphoramidite reagent of an appropriate label (Biotin, HEX etc.) in an automated DNA synthesizer is carried out. The labeled oligomers, obtained after cleavage and deprotection reactions, are analyzed on RP-HPLC. A distinctive feature of this protocol is the recovery of free oligomers from their labeled analogs under mild conditions. The oligomers obtained are comparable to the corresponding standard oligonucleotides (HPLC).

A two-step general technique for labeling of synthetic oligonucleotides is projected. To incorporate cleavable property in oligonucleotides, a new universal linker based on uridine nucleoside has been synthesized. The linkage between the label and the oligonucleotide is essentially stable under post-synthesis cleavage.Figure optionsDownload as PowerPoint slide