TABLE I.
Base sequences and nomenclature for the iCy3 monomer and (iCy3)2 dimer ss–dsDNA fork constructs used in these studies. The horizontal lines indicate regions of complementary base pairing.
| DNA construct | Nucleotide base sequence |
|---|---|
| +15 (iCy3)2 | 3′-GTC AGT ATT ATA CGC TCy3C GCT AAT ATA TAC GTT TTT TTT TTT TTT TTT TTT TTT TTT TTT T-5′ |
| dimer | 5′-CAG TCA TAA TAT GCG ACy3G CGA TTA TAT ATG CTT TTA CCA CTT TCA CTC ACG TGC TTA C-3′ |
| +15 iCy3 | 3′-GTC AGT ATT ATA CGC TCy3C GCT AAT ATA TAC GTT TTT TTT TTT TTT TTT TTT TTT TTT TTT T-5′ |
| monomer | 5′-CAG TCA TAA TAT GCG A T G CGA TTA TAT ATG CTT TTA CCA CTT TCA CTC ACG TGC TTA C-3′ |
| −1 (iCy3)2 | 3′-GAG GGA GCA CAG CAG AGG TCA GTA TTA TAC GCT Cy3CG CTG GTA TAC CAC GTT (T)28–5′ |
| dimer | 5′-CTC CCT CGT GTC GTC TCC AGT CAT AAT ATG CGA Cy3AT GCT TTT ACC ACT TTC ACT CAG GTG CTT A-3′ |
| −1 iCy3 | 3′-GAG GGA GCA CAG CAG AGG TCA GTA TTA TAC GCT Cy3CG CTG GTA TAC CAC GTT (T)28–5′ |
| monomer | 5′-CTC CCT CGT GTC GTC TCC AGT CAT AAT ATG CGA T AT GCT TTT ACC ACT TTC ACT CAG GTG CTT A-3′ |
| −2 (Cy3)2 | 3′-GAG GGA GCA CAG CAG AGG TCA GTA TTA TAC GCT Cy3CG CTG GTA TAC CAC GTT (T)28–5′ |
| dimer | 5′-CTC CCT CGT GTC GTC TCC AGT CAT AAT ATG CGC Cy3AT ACT TTC GCC ACT TTC ACT CAC GTG CTT A-3′ |
| +1 (Cy3)2 | 3′-GAG GGA GCA CAG CAG AGG TCA GTA TTA TAC GCT Cy3CG CTG GTA TAC CAC GTT (T)28–5′ |
| dimer | 5′-CTC CCT CGT GTC GTC TCC AGT CAT AAT ATG CGA Cy3GT ACT TTC GCC ACT TTC ACT CAC GTG CTT A-3′ |
| +2 (Cy3)2 | 3′-GAG GGA GCA CAG CAG AGG TCA GTA TTA TAC GCT Cy3CG CTG GTA TAC CAC GTT (T)28–5′ |
| dimer | 5′-CTC CCT CGT GTC GTC TCC AGT CAT AAT ATG CGA Cy3GC ACT TTC GCC ACT TTC ACT CAC GTG CTT A-3′ |