Figure 6. Demonstration of the fidelity of cDNA generation from chemically ligated tags using repeat-dependent bypass. A pair of doubly-conjugated oligonucleotides was prepared - one by the chemical ligation of two short oligonucleotides to a central oligonucleotide and the other by the chemical ligation of two long oligonucleotides to the same central oligonucleotide. The corresponding junction in each conjugate was flanked by the same repeated sequence. cDNA generation and subsequent PCR and electrophoresis using ethidium-stained agarose indicates that each of the conjugates may be amplified using relay primer-mediated bypass and that amplification occurs without the occurrence of homology-mediated shuffling, as indicated by the presence of bands with mobilities corresponding to amplification products containing “long-long” and “short-short” tag combinations, and the absence of the chimeric amplification products “long-short” and “short-long.”