Table 2.
Protein Data Bank database search results for the selection of ssDNA candidates.
| PMID | PDB ID | Chain Length | Sequence | QGRS | Exclude | Exclusion Criteria |
|---|---|---|---|---|---|---|
| 8069626 | 134D | 31 | TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT | 15 | Yes | Triplex |
| 8069626 | 135D | 31 | TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT | 15 | Yes | Triplex |
| 8069626 | 136D | 31 | TCCTCCTTTTTTAGGAGGATTTTTTGGTGGT | 15 | Yes | Triplex |
| 7613864 | 184D | 7 | GCATGCT | 0 | Yes | Dimer Quadruplex |
| 9737926 | 1A8N | 12 | GGGCTTTTGGGC | 0 | Yes | Dimer Quadruplex |
| 9737927 | 1A8W | 12 | GGGCTTTTGGGC | 0 | Yes | Dimer Quadruplex |
| 9092659 | 1AC7 | 16 | ATCCTAGTTATAGGAT | 0 | No | N/A |
| 9398169 | 1AO9 | 13 | GAGAGAXTCTCTC | 0 | Yes | Complexed with non-protein ligand |
| 7664126 | 1AU6 | 8 | CATGCATG | 0 | Yes | Complexed with non-protein ligand |
| 9384529 | 1AW4 | 27 | ACCTGGGGGAGTATTGCGGAGGAAGGT | 0 | Yes | Complexed with non-protein ligand |
| 9000625 | 1BJH | 11 | GTACAAAGTAC | 0 | No | N/A |
| 9367776 | 1C11 | 11 | TCCCGTTTCCA | 0 | Yes | Dimer Quadruplex |
| 12371856 | 1CS7 | 13 | GUTTTGXCAAAAC | 0 | Yes | Complexed with non-protein ligand |
| 2299669 | 1D16 | 16 | CGCGCGTTTTCGCGCG | 0 | Yes | Z-DNA |
| 10653638 | 1DB6 | 22 | CGACCAACGTGTCGCCTGGTCG | 0 | Yes | Complexed with non-protein ligand |
| 10756190 | 1DGO | 18 | AGGATCCTUTTGGATCCT | 0 | No | N/A |
| N/A | 1ECU | 19 | GCGCGAAACTGTTTCGCGC | 0 | No | N/A |
| 10924101 | 1EN1 | 18 | GTCCCTGTTCGGGCGCCA | 0 | No | N/A |
| 11090280 | 1EZN | 36 | CGTGCACCCGCTTGCGGCGACTTGTCGTTGTGCACG | 0 | Yes | Three way junction |
| 11790144 | 1FV8 | 11 | TATCATCGATA | 0 | Yes | Non-nucleotide modified residues |
| 11352724 | 1G5L | 6 | CCAAAG | 0 | Yes | Complexed with non-protein ligand |
| 11352724 | 1GJ2 | 6 | CCAAAG | 0 | Yes | Complexed with non-protein ligand |
| 11952790 | 1IDX | 18 | AGGATCCTTUTGGATCCT | 0 | No | N/A |
| 11952790 | 1II1 | 18 | AGGATCCUTTTGGATCCT | 0 | No | N/A |
| 11843626 | 1JU0 | 23 | CTTGCTGAAGCGCGCACGGCAAG | 0 | Yes | Dimer |
| 11843626 | 1JUA | 23 | CTTGCTGAAGCGCGCACGGCAAG | 0 | Yes | Dimer |
| 11991355 | 1JVE | 27 | CCTAATTATAACGAAGTTATAATTAGG | 0 | No | N/A |
| 12449414 | 1KR8 | 7 | GCGAAGC | 0 | No | N/A |
| 11895443 | 1L0R | 14 | ACGAAGTGCGAAGC | 0 | Yes | Complexed with non-protein ligand |
| 11849039 | 1LA8 | 13 | CGCGGTGTCCGCG | 0 | No | N/A |
| 11849039 | 1LAE | 13 | CGCGGTPTCCGCG | 0 | Yes | Non-nucleotide modified residues |
| 11849038 | 1LAI | 13 | CGCGGTGTCCGCG | 0 | Yes | Duplex |
| 11849038 | 1LAQ | 13 | CGCGGTPTCCGCG | 0 | Yes | Duplex |
| 11849038 | 1LAS | 13 | CGCGGTPTCCGCG | 0 | Yes | Duplex |
| 12560479 | 1MF5 | 7 | GCATGCT | 0 | Yes | Dimer Quadruplex |
| 12564921 | 1MP7 | 10 | GCCAGAGAGC | 0 | Yes | Complexed with non-protein ligand |
| 12755609 | 1NGO | 27 | CTCTTTTTGTAAGAAATACAAGGAGAG | 0 | No | N/A |
| 12755609 | 1NGU | 27 | CTCTCCTTGTATTTCTTACAAAAAGAG | 0 | No | N/A |
| 12758081 | 1P0U | 13 | GCATCGACGATGC | 0 | No | N/A |
| 8525381 | 1PNN | 24 | GAAGAAGAG | 0 | Yes | Triplex |
| 12449414 | 1PQT | 7 | GCGAAGC | 0 | No | N/A |
| 12952463 | 1PUY | 13 | GTTTTGXCAAAAC | 0 | Yes | Complexed with non-protein ligand |
| 10481034 | 1QE7 | 22 | CTAGAGGATCCTTTUGGATCCT | 0 | No | N/A |
| N/A | 1QYK | 7 | GCATGCT | 0 | Yes | Dimer Quadruplex |
| N/A | 1QYL | 7 | GCATGCT | 0 | Yes | Dimer Quadruplex |
| 15199171 | 1SNJ | 36 | CGTGCAGCGGCTTGCCGGCACTTGTGCTTCTGCACG | 0 | Yes | Three way junction |
| 14684897 | 1UE2 | 9 | GCGAAAGCT | 0 | Yes | Duplex |
| 14684897 | 1UE3 | 8 | GCGAAAGC | 0 | Yes | Duplex |
| 8901550 | 1XUE | 17 | GTGGAATGCAATGGAAC | 0 | No | N/A |
| 7583654 | 1ZHU | 10 | CAATGCAATG | 0 | No | N/A |
| 8548453 | 229D | 17 | CCAGACUGAAGAUCUGG | 0 | Yes | Non-nucleotide modified residues |
| 9818148 | 2ARG | 30 | TGACCAGGGCAAACGGTAGGTGAGTGGTCA | 18 | Yes | Complexed with non-protein ligand |
| 16620121 | 2AVH | 11 | GGGGTTTGGGG | 0 | Yes | G-Quadruplex |
| N/A | 2F1Q | 42 | GCACTGCATCCTTGGACGCTTGCGCCACTTGTGGTGCAGTGC | 0 | Yes | Four way junction |
| 16866556 | 2GKU | 24 | TTGGGTTAGGGTTAGGGTTAGGGA | 42 | Yes | G-Quadruplex |
| N/A | 2K67 | 17 | TTAATTTNNNAAATTAA | 0 | Yes | Non-nucleotide modified residues |
| N/A | 2K68 | 17 | TTAATTTNNNAAATTAA | 0 | Yes | Non-nucleotide modified residues |
| N/A | 2K69 | 17 | TTAATTTNNNAAATTAA | 0 | Yes | Non-nucleotide modified residues |
| 19374420 | 2K71 | 8 | GCGAAAGC | 0 | No | N/A |
| 19321501 | 2K8Z | 8 | TCGTTGCT | 0 | Yes | Dimer |
| 19070621 | 2KAZ | 13 | GGGACGTAGTGGG | 0 | Yes | Dimer Quadruplex |
| 21410196 | 2L13 | 13 | TATTATXATAATA | 0 | Yes | Non-nucleotide modified residues |
| 22129448 | 2L5K | 23 | CAGTTGATCCTTTGGATACCCTG | 0 | No | N/A |
| 22507054 | 2LO5 | 12 | GGCCGCAGTGCC | 0 | No | N/A |
| 22507054 | 2LO8 | 10 | GCCGCAGTGC | 0 | No | N/A |
| 22507054 | 2LOA | 10 | GCCGCAGTGC | 0 | Yes | Complexed with non-protein ligand |
| 22798499 | 2LSC | 12 | CGCGAAUUCGCG | 0 | Yes | Complexed with non-protein ligand |
| 23794476 | 2M8Y | 15 | CGCGAAGCATTCGCG | 0 | No | N/A |
| 23794476 | 2M8Z | 27 | GGTTGGCGCGAAGCATTCGCGGGTTGG | 9 | Yes | Quadruplex Duplex Hybrid |
| 23794476 | 2M90 | 32 | GCGCGAAGCATTCGCGGGGAGGTGGGGAAGGG | 21 | Yes | Quadruplex Duplex Hybrid |
| 23794476 | 2M91 | 30 | GGGAAGGGCGCGAAGCATTCGCGAGGTAGG | 7 | Yes | Quadruplex Duplex Hybrid |
| 23794476 | 2M92 | 34 | AGGGTGGGTGCTGGGGCGCGAAGCATTCGCGAGG | 17 | Yes | Quadruplex Duplex Hybrid |
| 23794476 | 2M93 | 32 | TTGGGTGGGCGCGAAGCATTCGCGGGGTGGGT | 29 | Yes | Quadruplex Duplex Hybrid |
| 8658168 | 2NEO | 19 | CCCGATGCXGCAATTCGGG | 0 | Yes | Complexed with non-protein ligand |
| 17362008 | 2O3M | 22 | AGGGAGGGCGCTGGGAGGAGGG | 39 | Yes | G-Quadruplex |
| 17388570 | 2OEY | 25 | CCATCGTCTACCTTTGGTAGGATGG | 0 | Yes | Complexed with non-protein ligand |
| 9020982 | 2PIK | 23 | CACTCCTGGTTTTTCCAGGAGTG | 0 | Yes | Complexed with non-protein ligand |
| 18515837 | 2VAH | 18 | AGGATCCTUTTGGATCCT | 0 | No | N/A |
| 18515837 | 2VAI | 18 | AGGATCCTUTTGGATCCT | 0 | No | N/A |
| 22287624 | 3QXR | 22 | AGGGAGGGCGCUGGGAGGAGGG | 39 | Yes | G-Quadruplex |
| N/A | 3T86 | 7 | GCATGCT | 0 | Yes | Complexed with non-protein ligand |
| 22409313 | 4DKZ | 12 | CGCGAAXXCGCG | 0 | Yes | Non-nucleotide modified residues |
| 8107090 | 148D | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 9384529 | 1AW4 | 27 | ACCTGGGGGAGTATTGCGGAGGAAGGT | 14 | Yes | Complexed with non-protein ligand |
| 9799703 | 1BUB | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 10756199 | 1C32 | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 10756199 | 1C34 | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 10756199 | 1C35 | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 10756199 | 1C38 | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 10653638 | 1DB6 | 22 | CGACCAACGTGTCGCCTGGTCG | 0 | Yes | Complexed with non-protein ligand |
| 8757801 | 1QDF | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 8757801 | 1QDH | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 15214802 | 1RDE | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 15637158 | 1Y8D | 16 | GGGGTGGGAGGAGGGT | 21 | Yes | Dimer Quadruplex |
| 9818148 | 2ARG | 30 | TGACCAGGGCAAACGGTAGGTGAGTGGTCA | 18 | Yes | Complexed with non-protein ligand |
| 17145716 | 2IDN | 15 | GGTTGGTGTGGTTGG | 20 | Yes | G-Quadruplex |
| 23935071 | 2M53 | 25 | TGTGGGGGTGGACGGGCCGGGTAGA | 21 | Yes | G-Quadruplex |
The details of the selection criteria are discussed in the text (see results section). For each experimentally resolved structure from the PDB database, denoted by its PDB ID, the table provides the corresponding publication denoted by its PubMed identifier (PMID), the sequence as provided in the PDB database, the chain length, the G-score denoted by QGRS obtained using the QGRS Mapper, and, if the DNA candidate was excluded from our list of potential candidates, the exclusion criteria.