Table 1. Molecular structures selected from the PDB, with PDB identification, number of structures in square brackets and tetraloop folding type (7,18), original authors, DNA or RNA sequences of PDB structures and of theoretical BCE models, and locations of the loop bases in the Major (M) groove, in the minor (m) groove, stacked in the central part of the helix (c) or in the solvent outside the structure (solv.).
| PDB identification | Authors | DNA or RNA sequence solved experimentally & sequence used in theoretical models | Na | Nb | Nc | Nd |
|---|---|---|---|---|---|---|
| DNA | ||||||
| 1ac7 [10] Type I | van Dongen et al. 1997 (15) | d(…ccta-GTTA-tagg…) & d(gcta-GTTA-tagc) | c/M | M | M / solv | c/m |
| 1bjh [16] | Chou et al. 1996 (16) | d(gtac-AAA-gtac) & d(gcac-AAA-gtgc) | c/M | M | c | - |
| 1xue [10] | Zhu et al. 1996 (30) | d(…gaat-GCA-atgg…) & d(gcat-GCA-atgc) | c/M | M | c | - |
| 1zhu [10] | Zhu et al. 1995 (38) | d(caat-GCA-atg) & d(gcat-GCA-atgc) | c/M | M | c | - |
| RNA | ||||||
| 1aud [31] Type II | Allain et al. 1997 (20) | r(…gucc-UUCG-ggac…) & r(gccc-UUCG-gggc) | c/M | m / solv | M | c |
| 1b36 [10] Type II | Butcher et al. 1999 (21) | r(…gcgc-UUCG-gcgc…) & r(gcgc-UUCG-gcgc) | c/M | m / solv | M | c |
| 1c0o [19] Type II | Colmenarejo and Tinoco 1999 (22) | r(…gguc-UUCG-gguc…) & r(gcuc-UUCG-gggc) | c/M | m / solv | M | c |
| 1hlx [20] Type II | Allain and Varani 1995 (17) | r(…uaac-UUCG-guug…) & r(gcac-UUCG-gugc) | c/M | m / solv | M | c |
Absence of fourth nucleotide in the loop is denoted (-). The loop bases are marked Na, Nb, Nc and Nd in the 5′ to 3′ direction.