Table 1. Duplex- and triplex-forming oligonucleotides used in this study.
| Name | Sequence (5′ to 3′) | Description | Structure | PDB ID |
|---|---|---|---|---|
| dslac | GA2T2GTGA(GC)2TCACA2T2C | Lac operon sequence | B-DNA | |
| ds26 | CA2TCG2ATCGA2T2CGATC2GAT2G | Synthetic construct | B-DNA | |
| ds14 | (CG)2A3T3(CG)2 | Synthetic construct | B-DNA (35) | 2DAU |
| ds10 | CGCA2T2GCG | Synthetic construct | B-DNA (36) | 1S23 |
| ds12-CG | CGT4A4CG | Synthetic construct | B-DNA (37) | 1RVI |
| ds12-GC | GCT4A4GC | Synthetic construct | B-DNA (37) | 1RVH |
| ds15-h | (CG)2A2GCAT2(CG)2 | Synthetic construct | B-DNA hairpin (38) | 2M8Y |
| ds17-TA | C2AGT2CGTAGTA2C3 | M.TaqI binding siteb | B-DNA (39) | |
| G3T2ACTACGA2CTG2 | ||||
| ds17-TTa | C2AGT2CGTAGTA2C3 | M.TaqI binding siteb | Mismatched B-DNA (39) | |
| G3T2ACTTCGA2CTG2 | ||||
| ds17-TCa | C2AGT2CGTAGTA2C3 | M.TaqI binding siteb | Mismatched B-DNA (39) | |
| G3T2ACTCCGA2CTG2 | ||||
| ds17-TGa | C2AGT2CGTAGTA2C3 | M.TaqI binding siteb | Mismatched B-DNA (39) | |
| G3T2ACTGCGA2CTG2 | ||||
| ds-A6 | G2CA6CG2 | Synthetic construct | A-tract bent B-DNA (40) | 1FZX |
| C2GT6GC2 | ||||
| ds-A6mut | G2CA2GA3CG2 | Synthetic construct | A-tract bent B-DNA (40) | 1G14 |
| C2GT3CT2GC2 | ||||
| ps-ds15 | A5TA2T3ATAT | Synthetic construct | Parallel duplex (41) | |
| T5AT2A3TATA | ||||
| ps-ds20 | T6A2T2A3TA2TA2T | Synthetic construct | Parallel duplex (41) | |
| A6T2A2T3AT2AT2A | ||||
| ps-ds24 | T10AT2A4T3ATA2 | Synthetic construct | Parallel duplex (41) | |
| A10TA2T4A3TAT2 | ||||
| PyW1 | TCT2CTCT3CT | Synthetic construct | Parallel triplex (42) | |
| PuC1 | AGA3GAGA2GA | |||
| PyH1 | TCT3CTCT2CT |
aThe bases in italics are mismatched.
bThe sequences contain the 4-bp recognition sequence of the DNA methyltransferase M.TaqI (5′-TCGY-3′, where Y = A for the natural substrate).