Mixed guanine, adenine base quartets: possible roles of protons and metal ions in their stabilization

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.Electronic supplementary materialThe online version of this article (10.1007/s00775-017-1507-7) contains supplementary material, which is available to authorized users.

A unified computational view of DNA duplex, triplex, quadruplex and their donor–acceptor interactions

“…The effect of the steric hindrance in MM pairs also can be observed by long mean HBL values, which are 1.98 Å for A–G, 1.97 Å for G–G, and 2.34 Å for A–A ( Supplementary Table S2 ). However, A–G and G–G have GVA close to 90°, so these purine-purine pairs have potential to seize each other in a square to form a tetrad ( 65 ). The T–T MM pair has a similar mean HBL to that of the G–T wobble pair ( Supplementary Table S2 ), but the T–T MM pair is less stable than the G–T wobble pair.…”

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“…Unfortunately, no tool is currently available to determine the G4s formed by other nucleotides than guanine residues. However, existence of such G4s in vitro has been documented [ 54 , 55 ].…”

“…Unfortunately, no tool is currently available to determine the G4s formed by other nucleotides than guanine residues. However, existence of such G4s in vitro has been documented [54,55]. The coloring of the nucleotides is default NDB (green for guanines, red for adenines, yellow for cytosines, and blue for thymines).…”

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“…Possible structures of such mixed quartets in the presence of either protons or alkali metal ions are discussed hinting at a putative two-metal motif [12].…”