Table 1.
All computed interactions are reported with the relative occurrence in cytosolic tRNA sequences from the Sprinzl database (60)
| Interaction | Occurrence | PDB | Res (Å) | Base pair | Burkard et al. | L&W | |
|---|---|---|---|---|---|---|---|
| 8–14–21 | U–A–A | 301 (82%) | 1ehz | 1.93 | uracil8…adenine14 | Reverse hoogsten (RH) | 4 |
| adenine14…adenine21 | – | – | |||||
| 9–12–23 | A–U–A | 170 (46%) | 1ehz | 1.93 | uracil12…adenine23 | Watson–Crick (WC) | 1 |
| adenine9…adenine23 | N7-amino,symmetric (N7as) | 4 | |||||
| 10–25–45 | G–C–G | 128 (35%) | 1ffy | 2.10 | guanine10…cytosine25 | Watson–Crick (WC) | 1 |
| guanine10…guanine45 | – | – | |||||
| m2G-C-G | 94 (25%) | 1ehz | 1.93 | N2-methylguanine10…cytosine25 | Watson–Crick (WC) | 1 | |
| N2-methylguanine10…guanine45 | – | – | |||||
| 13–22–46 | C–G–m7G | 179 (49%) | 1ehz | 1.93 | cytosine13…guanine22 | Watson–Crick (WC) | 1 |
| guanine22…7-methylguanine46 | N7-imino (N7i) | 4 | |||||
| C–G–G | 35 (9%) | 1j1u | 1.95 | C13…G22 | Watson–Crick | 1 | |
| guanine22…guanine46 | N7-imino (N7i) | 4 | |||||
| 15–48 | G–C | 186 (50%) | 1ehz | 1.93 | guanine15…cytosine48 | Reverse Watson–Crick (RWC) | 2 |
| 18–55 | G–Ψ | 349 (94%)a | 1ehz | 1.93 | guanine18…pseudouracil55 | imino-2-carbonyl, amino-2-carbonyl, bifurcatedb | 2 |
| G–U | 17 (19%) | 1j1u | 1.95 | guanine18…uracil55c | imino:amino-2-carbonyl, bifurcatedb | 2 | |
| 19–56 | G–C | 365 (99%)d | 1ehz | 1.93 | guanine19…cytosine56 | Watson–Crick (WC) | 1 |
| 26–44 | m22G–A | 94 (25%) | 1ehz | 1.93 | N2,N2-dimethylguanine26…adenine44 | Imino | 1 |
| G–A | 46 (12%) | 1j1u | 1.95 | guanine26…adenine44 | Imino | 1 | |
| 54–58 | T–A | 114 (31%) | 1c0a | 2.40 | thymine54…adenine58 | Reverse hoogsten (RH) | 4 |
| T–m1A | 84 (23%) | 1ehz | 1.93 | thymine54…1-methyladenine58 | Reverse hoogsten (RH) | 4 | |
| U–Ae | 34 (9%) | 1j1u | 1.95 | uracil54…adenine58 | Reverse hoogsten (RH) | 4 | |
| U–m1Ae | 23 (6%) | – | – | uracil54…1-methyladenine58 | Reverse hoogsten (RH) | 4 | |
PDB codes of the best resolution structure where each specific interaction is observed are also reported. For all computed base pairs with at least two hydrogen bonds, classification is given according to Burkard et al. (73) and Leontis and Westhof (74) schemes; in (74) ‘1’ stays for Cis Watson–Crick/Watson–Crick Antiparallel, ‘2’ for Trans Watson–Crick/Watson–Crick Parallel and ‘4’ for Trans Watson–Crick/Hoogsteen Antiparallel. Bases nomenclature is according to Sprinzl et al. (59).
a71 sequences bear an additional methyl group on the ribose O2′ atom of guanosine18.
bNomenclature from the NCIR database, http://prion.bchs.uh.edu/bp_type/ (75).
cComputed starting from the 1j1u coordinates.
d51 sequences bear an additional methyl group on the ribose O2′ atom of guanosine19 or cytidine56.
eThese are the fourth and fifth most populated nucleic acid base combinations, after 1-methylpseudouracil54-adenine 58 (m1Ψ-A), present in39 sequences (11%).