Table 1. Self-priming template hairpin sequences and their designations.
 | ||
|---|---|---|
| Deoxyoligonucleotide sequence | Template sequence | Hairpin designation |
| G·CH(A)n series | ||
| AGCTACTTTCCTTTTTGGAAAGTAGC | 1A | G·CH1A |
| AAGCTACTTTCCTTTTTGGAAAGTAGC | 2A | G·CH2A |
| AAAGCTACTTTCCTTTTTGGAAAGTAGC | 3A | G·CH3A |
| AAAAGCTACTTTCCTTTTTGGAAAGTAGC | 4A | G·CH4A |
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGC | 5A | G·CH5A |
| G·CH(A·T)n series | ||
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCT | 4A | G·CH5A·1T |
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCTT | 3A | G·CH5A·2T |
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCTTT | 2A | G·CH5A·3T |
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCTTTT | 1A | G·CH5A·4T |
| T·AH | ||
| AAAAATCTACTTTCCTTTTTGGAAAGTAGA | 5A | T·AH5A |
| G·CH(T)1,5 | ||
| TTTTTGCTACTTTCCTTTTTGGAAAGTAGC | 5T | G·CH5T |
| TGCTACTTTCCTTTTTGGAAAGTAGC | 1T | G·CH1T |
| Terminated | ||
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCdT | NE | G·CH5A·dT |
| Fully extended | ||
| AAAAAGCTACTTTCCTTTTTGGAAAGTAGCTTTTT | NE | G·CH5A·5T |
The standard stem—loop structure of the template—primer hairpins is comprised of the sequence (from 5′ to 3′) 5′-GCTACTTTCC(T)5GGAAAGTAGC-3′, in which the template—primer termini consist of G·C base pairs (except for T·AH5A, in which the template—primer terminus is a T·A). The loop consists of 5Ts with a C·G closing base pair, and the underlined segments comprise the base-paired stem region. The bases in bold (within the sequences) correspond to the 5′ single-strand template region. NE, not extendable. The following guidelines have been employed for the hairpin designations. The first two letters (e.g., G·C) and an H (hairpin) refer to the template-primer terminal junction, followed by the number and identity of the template single-strand bases (e.g., 5A). In several hairpins, the stem region is extended with additional base pairs [i.e., G·CH(A·T)n series].