Skip to main content
. 2006 Oct 23;27(1):20–30. doi: 10.1128/MCB.00824-06

FIG. 1.

FIG. 1.

Sequences of the DNA substrates used in binding and activity assays. All substrates used in activity assays contain a single cytidine within the bubble and differ in the dinucleotide immediately upstream of the target cytidine constituting either WRC motifs (hot spots) or non-WRC motifs (cold spots). *, radioactively labeled strand; HS, bubble containing a hot-spot motif; CS, bubble containing a cold-spot motif. The last number of each substrate indicates the size of the single-stranded bubble portion. The position of the target cytidine within the bubble is indicated by an arrow for HS1bub5. HS4bub9 and CS4bub9 contain repeats of the hot-spot sequence AAC and the cold-spot CCC, respectively, and were used as unlabeled competitors in activity assays. The single-stranded substrates HS5ss and CS5ss containing tandem repeats of hot or cold spots were used in EMSAs as well as NECEEM assays to measure AID binding. AGUbub and GGUbub are analogous to HS1bub7 and CS3bub7 except for the substitution of uridine for cytidine.