Table 1.
Sequences of oligonucleotides used in experiments
| Name | Sequence (5′→3′) | Internal lesiona | Substrate for: |
|---|---|---|---|
| URA03 | (P)CACGAA(U)CAACTCAGCAACTCCtt(NH2)b,c,d,e | Uracil (U) | UDG |
| HX02 | (P)CACGAA(X)CAACTCAGCAACTCCtt(NH2)f | Hypoxanthine (X) | AAG |
| AP02 | (P)CACGAA(B)CAACTCAGCAACTCCtt(NH2)g | Tetrahydrofuran (B) | AP incision |
| Contr01 | (P)CACGAATCAACTCAGCAACTCCtt(NH2) | n/a | n/a |
| GAP04 | (P)CAACTCAGCAACTCCtt(NH2) | Single nucleotide gap | DNA polymerase |
| LIG03 | (P)TCAACTCAGCAACTCCtt(NH2) | Ligatable SSB | DNA ligase |
| Loop01Aflc | (flc)ttGGAGTTGCTGAGTTGATTCGTGAGCACCAACCGGTGCTh | n/a | n/a |
| Loop01Aird | (ird)ttGGAGTTGCTGAGTTGATTCGTGAGCACCAACCGGTGCTi | n/a | n/a |
| Loop01Cflc | (flc)ttGGAGTTGCTGAGTTGCTTCGTGAGCACCAACCGGTGCT | n/a | n/a |
| Loop01Gflc | (flc)ttGGAGTTGCTGAGTTGGTTCGTGAGCACCAACCGGTGCT | n/a | n/a |
| Loop01Tflc | (flc)ttGGAGTTGCTGAGTTGTTTCGTGAGCACCAACCGGTGCT | n/a | n/a |
| Loop02 | (flc)ttGGAGTTGCTGAGTTGATTCGTGAGCACCAACCGGTGCTCACGAA | n/a | n/a |
aInternal lesion present in oligonucleotide or in final substrate complex.
bP indicates phosphorylation.
cNH2 indicates amino modifier group.
dU indicates uracil.
elower case letters indicate nucleotides linked via phosphorothiate bonds.
fX indicates hypoxanthine.
gB indicates tetrahydrofuran.
hflc indicates fluorescein.
iird indicates IRDye®.