FIG. 5.

Blocking oligomers and their effect on transfer efficiency with the UTR and SNP-2 templates. (A) Schematic of the UTR donor template and the DNA oligomers designed to block invasion. Nucleotide positions within the genomic RNA to which the donor template corresponds are indicated and represent the region of homology shared between the donor and acceptor templates. Open circles on the donor indicate relative positions at which donor and acceptor differ in sequence by single- or double-nucleotide bases and are designated markers 1 to 6. Hatched lines on either end of the template represent plasmid-derived sequences. The 35-nt DIS hairpin site is indicated. The arrow at the 3′ end of the template represents the DNA primer and indicates the direction of synthesis. Blocking oligomers are designated by the template regions that they span and are aligned opposite their homologous regions on the template. BP162-187 falls outside the region of homology. (B) Transfer assays were performed for 60 min with the WT UTR and SNP-2 templates in the presence of 0.5 pmol of the blocking oligomer (see Materials and Methods for details). Transfer efficiency in the absence of blocking oligomers was taken as 100% (Ctrl). Transfer efficiency measured in the presence of each blocking oligomer was plotted as a percentage of the control reaction. Values were averaged from a minimum of three independent experiments.