Table 2. Selected G-quadruplex and i-motif-forming sequences used in this study.
| Name | Sequence (5′ to 3′) | Description | Structurea | PDB ID |
|---|---|---|---|---|
| 21GG | G3(TTAG3)3 | Human telomere | Polymorphic (43–45)b | |
| 22AG | AG3(TTAG3)3 | Human telomere | Hybrid 3+1 (45–47) | |
| 23AG | AG3(TTAG3)3T | Human telomere | Hybrid 3+1 (45–47) | 2KKAc |
| 24TTG | TTG3(TTAG3)3A | Modified human telomere | Hybrid 3+1 (43) | 2GKU |
| 25TAG | TAG3(TTAG3)3ATT | Human telomere | Hybrid 3+1 (48) | 2JSL |
| 45AG | G3(TTAG3)7 | Human telomere | Hybrid 3+1 (49) | |
| Oxy30 | T(G4T4)3G4T | Oxytricha telomere | Hybrid 3+1d | |
| Oxy28 | (G4T4)3G4 | Oxytricha telomere | Antiparallel (50)/ hybrid 3+1d,e | 201D |
| c-myc | TGAG3TG3TAG3TG3TA2 | c-myc promoter | Parallel (51) | 1XAV |
| c-kit1 | G3AG3CGCTG3AG2AG3 | c-kit promoter | Parallel (52,53)d | |
| c-kit87-up | AG3AG3CGCTG3AG2AG3 | c-kit promoter | Parallel with a snapback featured (54) | 2O3M |
| c-kit2 | CG3CG3CGCTAG3AG3T | c-kit promoter | Monomeric parallel / dimeric paralleld (55) | 2KYP/2KYO |
| c-kit2GG | G3CG3CGCTAG3AG3 | c-kit promoter | Paralleld (52) | |
| c-kit* | G2CGAG2AG4CGTG2C2G2C | c-kit promoter (SP1 binding site) | Antiparallel (56) | |
| B-raf | G3CG4AG5A2G3A | B-raf promoter | Parallel intertwined dimer (57)d | 4H29 |
| K-ras 35B3 | AG3CG2TGTG3A2GAG3A2GAG5AG2 | K-ras promoter | Paralleld | |
| K-ras 35B1 | AG3CG2TGTG3A2GAG3A2GAG5AG2CAG | K-ras promoter | Paralleld | |
| N-myc | TAG3CG3AG3AG3A2 | N-myc intron | Monomeric parallel / dimeric parallel (58) | 2LED/2LEE |
| pilE-NG16 | G3TG3T2G3TG3 | N. gonorrhoeae pilin expression locus | Parallel monomer / stacked dimer (59) | 2LXV |
| pilE-NG22 | TAG3TG3T2G3TG4A2T | N. gonorrhoeae pilin expression locus | Parallel (59) | 2LXQ |
| G4CT | (G4CT)3G4 | Treponema pallidum genome | Mainly antiparallelf (60) | |
| T30177-TT | T2GTG2TG3TG3TG3T | Aptamer (HIV-1 integrase inhibitor) | Parallel, with bulge (61) | 2M4P |
| T95–2T | T2G3TG3TG3TG3T | Aptamer (HIV-1 integrase inhibitor) | Parallel monomer / stacked dimer (62) | 2LK7 |
| 93del | G4TG3AG2AG3T | Aptamer (HIV-1 integrase inhibitor) | Interlocked bimolecular dimeric paralleld (63) | 1Y8D |
| J19 | GIGTG3TG3TG3T | Aptamer (HIV-1 integrase inhibitor) | Parallel monomer / stacked dimerd (64) | 2LE6 |
| 25CEB | AG3TG3TGTA2GTGTG3TG3T | 25CEB human minisatellite locus | Paralleld | |
| 26CEB | A2G3TG3TGTA2GTGTG3TG3T | 25CEB human minisatellite locus | Paralleld (65) | 2LPW |
| TBA | G2T2G2TGTG2T2G2 | Aptamer (thrombin) | Antiparallel (66) | 148D |
| H-Bi-G4 | G3ACGTAGTG3 | Synthetic construct | Bimolecular, antiparallel, with hairpin loopsd (67) | 2KAZ |
| 161T | TG3TG3T6G3TG3T | Synthetic construct | Paralleld | |
| 161TT | T2G3TG3T6G3TG3T2 | Synthetic construct | Paralleld | |
| 222T | TG3T2G3T2G3T2G3T | Synthetic construct | Paralleld | |
| 222TT | T2G3T2G3T2G3T2G3T2 | Synthetic construct | Paralleld | |
| [TG4T]4 | TG4T | Synthetic construct | Tetramolecular parallel (68) | 2O4F |
| [TG5T]4 | TG5T | Synthetic construct | Tetramolecular parallel | |
| [AG4T]4 | AG4T | Synthetic construct | Tetramolecular parallel | |
| [AG5T]4 | AG5T | Synthetic construct | Tetramolecular parallel | |
| Mito9 | TG6TGTCT3G4T3(G2T2)2CG4TATG4T | Human mitochondrial DNA | Unknown | |
| Mito86 | TGT2AG4TCATG3CTG3T | Human mitochondrial DNA | Unknown | |
| 21CC | C3(TA2C3)3 | Human telomere | i-motif (69) | |
| 22Py | A2TC3AC4TC3AC4T2 | c-myc promoter | i-motif (70) | |
| 24mutHtelo | (TTACCG)4 | Mutated human telomere | Unfolded | |
| 22mutHtelo1234 | AGTG(T2AGTG)3 | Mutated human telomere | Unfolded | |
| 22mutHtelo23 | AG3(T2AGTG)2T2AG3 | Mutated human telomere | Unfolded (71) |
aReferences link to a structure determination by either NMR, X-ray or CD spectroscopy.
bHybrid 3+1 at high strand concentration and antiparallel at low (3 μM) strand concentration. Addition of flanking bases promotes the hybrid 3+1 conformation (e.g. 22AG, 23AG, 24TTG, 25TAG).
c2KKA was obtained following a dG14 to dI14 mutation of 23AG, the corresponding 2-quartet structure will thus not be discussed for the calibration.
dRelative strand orientation observed by CD: see experimental section and Supplementary Figure S3.
eA hybrid 3+1 conformation is observed by CD, which could be caused by a difference in cation (Na+ in the PDB entry).
fMainly monomolecular in our conditions (100 mM KCl). A tetramolecular structure is formed with increasing KCl concentration (60).