Table 2. Sequences of 3-MI-containing oligonucleotides (5′→3′) used to determine the minimum length of strand for an optimal change in fluorescence intensity upon bulge formation.
| Name | Oligonucleotide sequence (5′→3′) | Fold fluorescence increase |
|---|---|---|
| HIVPCR-11 | aataaFaatag | 1.1 |
| HIVPCR-13 | aaataaFaatagt | 1.2 |
| HIVPCR-15 | taaataaFaatagta | 1.2 |
| HIVPCR-18 | taaataaFaatagtaAga | 7.9 |
| HIVPCR-21 | taaataaFaatagtaAgaatg | 13.6 |
| HIVPCR-24 | taaataaFaatagtaAgaatgtat | 13.6 |
Each of the 3-MI-containing strands was paired to complementary strands in which 3-MI did not have a base pairing partner.