Differential stabilization of adenine quartets by anions and cations

Abstract

We have investigated the structures and stabilities of four different adenine quartets with alkali and halide ions in the gas phase and in water, using dispersion-corrected density functional theory at the BLYP-D/TZ2P level. First, we examine the empty quartets and how they interact with alkali cations and halide anions with formation of adenine quartet–ion complexes. Second, we examine the interaction in a stack, in which a planar adenine quartet interacts with a cation or anion in the periphery as well as in the center of the quartet. Interestingly, for the latter situation, we find that both cations and anions can stabilize a planar adenine quartet in a stack.Electronic supplementary materialThe online version of this article (doi:10.1007/s00775-009-0611-8) contains supplementary material, which is available to authorized users.

3-Substituted xanthines as promising candidates for quadruplex formation: computational, synthetic and analytical studies

“…[4][5][6] So far, several modifications have been suggested in the guanine motif, and the formed quadruplex structures have been experimentally examined. 7,8 Other purines (adenine, [9][10][11][12] hypoxanthine 8,[13][14][15][16] ) and pyrimidines (uracil, [17][18][19] thymine, 20 cytosine [21][22][23] ) have also been investigated experimentally and computationally as building blocks of quadruplex structures. In all of these cases, the neighboring heterocycles are connected by only one H-bond in the tetrad structures, causing a weaker interaction and a less planar geometry than in guanine tetrads.…”

Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity

“…The planarization energy of A 4 -N3 and A 4 -N7 was found to be 0.2 and 11 kcal mol À1 , respectively, while for A 4 -N1 system it was 22.3 kcal mol À1 . 28 The low stability of planar A 4 -N1 quartet is probably a main reason why this type of quartet has not been characterized by X-ray crystallography in contrast to A 4 -N3 29 and A 4 -N7. 20 Selected substituents, varying in their electronic properties (X ¼ NO 2 , Cl, F, H, Me, NH 2 ), were inserted into each adenine molecule at the same position within a certain quartet.…”

Berberrubine Phosphate: A Selective Fluorescent Probe for Quadruplex DNA

“…Therefore, the π-stacked ligand has further opportunities to bind with the phosphate to the amino substituents in the loops of 22AG and a2. Furthermore, 22AG contains an adenine triplet above the terminal G-quartet, which offers an additional binding site for the phosphate group because it has been shown that anions bind well to the adenine quartet [45,46]. In contrast, no ICD signals of ligand 2 were observed in the presence of 22AG and a2, which is often proposed to indicate terminal π stacking [73,74], also in the case of the parent berberine 1a [28,75].…”

“…In this context, we focused our attention to anionic substituents. Based on the observation that anions can coordinate to specific binding sites of DNA [ 43 , 44 , 45 , 46 ], we reasoned that a substitution of berberine with anionic substituents may also result in particular binding modes, which in turn would cause distinct light-up effects. However, to the best of our knowledge, the DNA-binding properties of only a few DNA ligands with anionic substituents have been investigated and it has been found that these ligands exhibit a negligible affinity toward double-stranded DNA, which is supposedly caused by the strong repulsion between the negatively charged ligands and the phosphate backbone of the DNA [ 47 , 48 , 49 ].…”