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. 2004 Jan 12;32(1):e8. doi: 10.1093/nar/gng155

Figure 1.

Figure 1

Figure 1

Figure 1

UDG selection scheme. (A) The DNA template for the UDG selection assay is GC-rich and 80 bp in length. An AT-rich region juxtaposed with a degenerate region constitute the compound test site. Correspondingly, a test compound consists of an AT-binding cassette (black circles) juxtaposed with an experimental portion of unknown specificity (white shapes). Typically, two T residues in the bottom strand of the test site are substituted by U. This serves as a UDG-sensitive probe for compound binding. The duplex oligonucleotide with the sequence drawn here is written as N(9)AAAA·UUTT. Separately, several U residues are embedded in the top strand near the 5′ end of the template to prevent the top strand from being amplified. The upstream U residues are embedded in a GC-rich region which constitutes a poor compound binding site. The drawing is not to scale. (B) The U residues are maintained through successive rounds of selection by including them in the PCR primers. (C) U residues in the template are removed by UDG except those protected by compound binding. Templates with abasic sites, such as the top and bottom unbound strands, are not amplified.