Protonated nucleobases are not fully ionized in their chloride salt crystals and form metastable base pairs further stabilized by the surrounding anions.
ABSTRACT: This paper presents experimental charge-density studies of cytosinium chloride, adeninium chloride hemihydrate and guaninium dichloride crystals based on ultra-high-resolution X-ray diffraction data and extensive theoretical calculations. The results confirm that the cohesive energies of the studied systems are dominated by contributions from intermolecular electrostatic interactions, as expected for ionic crystals. Electrostatic interaction energies (Ees) usually constitute 95% of the total interaction energy. The Ees energies in this study were several times larger in absolute value when compared, for example, with dimers of neutral nucleobases. However, they were not as large as some theoretical calculations have predicted. This was because the molecules appeared not to be fully ionized in the studied crystals. Apart from charge transfer from chlorine to the protonated nucleobases, small but visible charge redistribution within the nucleobase cations was observed. Some dimers of singly protonated bases in the studied crystals, namely a cytosinium-cytosinium trans sugar/sugar edge pair and an adeninium-adeninium trans Hoogsteen/Hoogsteen edge pair, exhibited attractive interactions (negative values of Ees) or unusually low repulsion despite identical molecular charges. The pairs are metastable as a result of strong hydrogen bonding between bases which overcompensates the overall cation-cation repulsion, the latter being weakened due to charge transfer and molecular charge-density polarization.
Project description:In the title compound, C(5)H(6)N(5) (+)·C(4)H(6)N(3)O(+)·SO(4) (2-), the adeninium (AdH(+)) and cytosinium (CytH(+)) cations and sulfate dianion are involved in a three-dimensional hydrogen-bonding network with four different modes, viz. AdH(+)?AdH(+), AdH(+)?CytH(+), AdH(+)?SO(4) (2-) and CytH(+)?SO(4) (2-). The adeninium cations form N-H?N dimers through the Hoogsteen faces, generating a characteristic R(2) (2)(10) motif. This AdH(+)?AdH(+) hydrogen bond in combination with AdH(+)?CytH(+ )H-bonds leads to two-dimensional cationic ribbons parallel to the a axis. The sulfate anions inter-link the ribbons into a three-dimensional hydrogen-bonding network and thus reinforce the crystal structure.
Project description: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.
Project description:Interaction of H2O, H2S, H2Se, NH3, PH3, and AsH3 with cations H+, CH3 +, Cu+, Al+, Li+, Na+, and K+ was studied from the energetic and structural viewpoint using B3LYP/6-311++G(d,p) method. The charge transfer from the Lewis bases to the cations reduces lone pair/lone pair (LP/LP) repulsion in H2O, H2S, and H2Se and LP/bond pair (LP/BP) repulsion in NH3, PH3, and AsH3. In parallel, changes in the H-M-H angles (M = O, S, Se, N, P, and As) are observed. The change in the H-M-H angle during the interactions was proportional to the amount of charge transferred from the bases to the cations and electron density (?) at the molecule/cation bond critical point. Also, the opposite trend for proton affinities of these two families, that is, NH3 > PH3 > AsH3 and H2O < H2S < H2Se, was interpreted on the basis of LP/BP repulsion in their neutral and protonated forms. Interaction of the Lewis bases with neutral Lewis acids including BeH2, BeF2, and BH3 was studied energetically and structurally. The calculated energies for interactions of H2O and NH3 with BeH2, BeF2, and BH3 are larger than the corresponding values for H2S, H2Se, PH3, and AsH3. This difference was interpreted on the basis of the lower stability of H2O and NH3 because of large LP/LP and LP/BP repulsion in H2O and LP/BP repulsion in NH3.
Project description:Oligonucleotide-directed triple helix formation has been recognized as a potential tool for targeting genes with high specificity. Cystosine methylation in the 5' position is both ubiquitous and a stable regulatory modification, which could potentially stabilize triple helix formation. In this work, we have used a combination of calorimetric and spectroscopic techniques to study the intramolecular unfolding of four triplexes and two duplexes. We used the following triplex control sequence, named Control Tri, d(AGAGAC5TCTCTC5TCTCT), where C5 are loops of five cytosines. From this sequence, we studied three other sequences with dC ? d(m5C) substitutions on the Hoogsteen strand (2MeH), Crick strand (2MeC) and both strands (4MeHC). Calorimetric studies determined that methylation does increase the thermal and enthalpic stability, leading to an overall favorable free energy, and that this increased stability is cumulative, i.e. methylation on both the Hoogsteen and Crick strands yields the largest favorable free energy. The differential uptake of protons, counterions and water was determined. It was found that methylation increases cytosine protonation by shifting the apparent pKa value to a higher pH; this increase in proton uptake coincides with a release of counterions during folding of the triplex, likely due to repulsion from the increased positive charge from the protonated cytosines. The immobilization of water was not affected for triplexes with methylated cytosines on their Hoogsteen or Crick strands, but was seen for the triplex where both strands are methylated. This may be due to the alignment in the major groove of the methyl groups on the cytosines with the methyl groups on the thymines which causes an increase in structural water along the spine of the triplex.
Project description:In the title proton-transfer organic salt, C5H6.3N5 (+)·C8H4.7O4 (-)·C3H7NO, the adeninium moiety is protonated at the N atom in the 1-position of the 6-amino-7H-purin-1-ium (adeninium) cation. In the solid state, the second acidic proton of isophthalic acid is partially transferred to the imidazole N atom of the adeninium cation [refined O-H versus N-H ratio = 0.70?(11):0.30?(11)]. Through the partially transferred proton, the adeninium cation is strongly hydrogen bonded (N-H?O/O-H?N) to the isophthalate anion. This strong inter-action is assisted by another N-H?O hydrogen bond originating from the adeninium NH2 group towards the isophthalate keto O atom, with an R (2) 2(8) graph-set motif. This arrangement is linked via N-H?O hydrogen bonds to the O atoms of the carboxyl-ate group of an isophthalate anion. Together, these hydrogen bonds lead to the formation criss-cross zigzag isophthalate?adeninium chains lying parallel to (501) and (50-1). The adeninium cations and the isophthalate anions are arranged in infinite ? stacks that extend along the c-axis direction [inter-planar distance = 3.305?(3)?Å]. Mol-ecules are inclined with respect to this direction and within the stacks they are offset by ca. half a mol-ecule each. Combination of the N-H?O and O-H?N hydrogen bonds with the ?-? inter-actions forms infinitely stacked isophthalate?adeninium chains, thus leading to a two-dimensional supra-molecular structure with parallel inter-digitating layers formed by the ? stacked isophthalate?adeninium chains. The DMF mol-ecules of crystallization are bonded to the adeninium cations through strong N-H?O hydrogen bonds and project into the lattice space in between the anions and cations. There are also C-H?O hydrogen bonds present which, combined with the other inter-actions, form a three-dimensional network. The crystal under investigation was found to be split and was handled as if non-merohedrally twinned.
Project description:Targeting and invading double-stranded DNA with synthetic oligonucleotides under physiological conditions remain a challenge. Bis-locked nucleic acids (bisLNAs) are clamp-forming oligonucleotides able to invade into supercoiled DNA via combined Hoogsteen and Watson-Crick binding. To improve the bisLNA design, we investigated its mechanism of binding. Our results suggest that bisLNAs bind via Hoogsteen-arm first, followed by Watson-Crick arm invasion, initiated at the tail. Based on this proposed hybridization mechanism, we designed next-generation bisLNAs with a novel linker able to stack to adjacent nucleobases, a new strategy previously not applied for any type of clamp-constructs. Although the Hoogsteen-arm limits the invasion, upon incorporation of the stacking linker, bisLNA invasion is significantly more efficient than for non-clamp, or nucleotide-linker containing LNA-constructs. Further improvements were obtained by substituting LNA with 2'-glycylamino-LNA, contributing a positive charge. For regular bisLNAs a 14-nt tail significantly enhances invasion. However, when two stacking linkers were incorporated, tail-less bisLNAs were able to efficiently invade. Finally, successful targeting of plasmids inside bacteria clearly demonstrates that strand invasion can take place in a biologically relevant context.
Project description:Charged nucleobases have been found to occur in several known RNA molecules and are considered essential for their structure and function. The mechanism of their involvement is however not yet fully understood. Revelation of the role of N7-protonated guanine, in modulating the geometry and stability of noncanonical base pairs formed through its unprotonated edges [Watson-Crick (WC) and sugar], has triggered the need to evaluate the feasibility of similar roles of other protonated nucleobases [Halder et al., Phys Chem Chem Phys, 2015, 17, 26249]. In this context, N3 protonation of guanine makes an interesting case as its influence on the charge distribution of the WC edge is similar to that of N7 protonation, though its thermodynamic cost of protonation is significantly higher. In this work, we have carried out structural bioinformatics analyses and quantum mechanics-based calculations to show that N3 protonation of guanine may take place in a cellular environment, at least in the G:C W:W Trans and G:G W:H Cis base pairs. Our results provide a reasonable starting point for future investigations in order to address the larger mechanistic question.
Project description:The asymmetric unit of the title compound, 2C5H6N5 (+)·SiF6 (2-)·2H2O, contains one adeninium cation, half of a hexa-fluorido-silicate anion located on an inversion centre and one lattice water mol-ecule. The adeninium cations are connected through N-H?N hydrogen bonds involving one H atom of the -NH2 group and the H atom of the protonated N atom of the adenine ring system, forming centrosymmetric ring motifs of the type R 2 (2)(10) and R 2 (2)(8), respectively. The overall connection of the cation leads to the formation of planar ribbons parallel to (122). In the ribbons, slipped ?-? stacking inter-actions, with a centroid-to-centroid distance of 3.6938?(9)?Å, an inter-planar distance of 3.455?Å and a slippage of 1.306?Å is observed. The hexa-fluorido-silicate anion and the water mol-ecule are linked through O-H?F hydrogen bonds [ring motif R 4 (4)(12)] into chains parallel to . The cationic ribbons and anionic chains are finally connected through additional N-H?O, N-H?F and O-H?F hydrogen bonds into a three-dimensional network in which layers of adeninium cations and fluorido-silicate anions alternate parallel to (001).
Project description:Ribozymes employ diverse catalytic strategies in their self-cleavage mechanisms, including the use of divalent metal ions. This work explores the effects of Mg2+ ions in the active site of the glmS ribozyme-GlcN6P cofactor complex using computational methods. Deleterious and potentially beneficial effects of an active site Mg2+ ion on the self-cleavage reaction were identified. The presence of a Mg2+ ion near the scissile phosphate oxygen atoms at the cleavage site was determined to be deleterious, and thereby anticatalytic, due to electrostatic repulsion of the cofactor, disruption of key hydrogen-bonding interactions, and obstruction of nucleophilic attack. On the other hand, the presence of a Mg2+ ion at another position in the active site, the Hoogsteen face of the putative base, was found to avoid these deleterious effects and to be potentially catalytically favorable owing to the stabilization of negative charge and pKa shifting of the guanine base.
Project description:NMR relaxation dispersion studies have shown that Watson-Crick G-C and A-T base pairs in duplex DNA exist in dynamic equilibrium with their Hoogsteen counterparts. Hoogsteen base pairs form through concurrent rotation of the purine base about the glycosidic bond from an anti to a syn conformation and constriction of the C1'-C1' distance across the base pair by ?2?Å to allow Hoogsteen type hydrogen bonding. Owing to their unique structure, Hoogsteen base pairs can play important roles in DNA recognition, the accommodation, recognition, and repair of DNA damage, and in DNA replication. NMR relaxation dispersion experiments targeting imino nitrogen and protonated base and sugar carbons have provided insights into many structural features of transient Hoogsteen base pairs, including one of two predicted hydrogen bonds involving (G)N7···H-N3(C)+ and (A)N7···H-N3(T). Here, through measurement of cytosine amino (N4) R1? relaxation dispersion, we provide direct evidence for the second (G)O6···H2-N4(C)+ hydrogen bond in G(syn)-C+ transient Hoogsteen base pairs. The utility of cytosine N4 R1? relaxation dispersion as a new sensitive probe of transient Hoogsteen base pairs, and cytosine dynamics in general, is further demonstrated by measuring G(syn)-C+ Hoogsteen exchange near neutral pH and in the context of the naturally occurring DNA modification 5-methyl cytosine (m5C), in DNA samples prepared using chemical synthesis and a 15N labeled m5C phosphoramidite.