Abstract
Structural variations of the well-known guanine quartet (G4) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past. Here, possible structures of mixed AGAG quartets both in the presence of protons and alkali metal ions are discussed, and in particular, the existence of a putative four-purine, two-metal motif.
Original language | English |
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Pages (from-to) | 41-49 |
Number of pages | 9 |
Journal | JBIC : Journal of Biological Inorganic Chemistry |
Volume | 23 |
Issue number | 1 |
DOIs | |
Publication status | Published - 1 Jan 2018 |
Funding
Acknowledgements This work was supported by the Deutsche Forschungsgemeinschaft, DFG (PML, BL), and the Netherlands Organization for Scientific Research, NWO (CFG). We dedicate this paper to Professor Helmut Sigel, Basel, at the occasion of his 80th birthday, with thanks to numerous inspirations, excellent collaborations, and above all, for his friendship.
Keywords
- Alkali metal ions
- DFT calculations
- Guanine quartets
- Mixed adenine
- Protonated adenine