The effects of cobalt-hexammine and cobalt-pentammine cations on the solution structure of calf-thymus DNA. DNA condensation and structural features studied by FTIR difference spectroscopy

Investigations of the Cobalt Hexamine Uranyl Carbonate System: Understanding the Influence of Charge and Hydrogen Bonding on the Modification of Vibrational Modes in Uranyl Compounds

Hydrogen bonding networks within hexavalent uranium materials are complex and may influence the overall physical and chemical properties of the system. This is particularly true if hydrogen bonding takes places between the donor and the oxo group associated with the uranyl cation (UO₂²⁺). In the current study, we evaluate the impact of charge-assisted hydrogen bonding on the vibrational modes of the uranyl cation using uranyl tricarbonate [UO₂(CO₃)₃]^4- interactions with [Co(NH₃)₆]³⁺ as the model system. Herein, we report the synthesis and structural characterization of five novel compounds, [Co(NH₃)₆]Cl(CO₃) (Co_Cl_CO₃), [Co(NH₃)₆]₄[UO₂(CO₃)₃]₃(H₂O)_11.67 (Co4U3), [Co(NH₃)₆]₃[UO₂(CO₃)₃]₂Cl (H₂O)_7.5 (Co3U2_Cl), [Co(NH₃)₆]₂[UO₂(CO₃)₃]Cl₂ (Co2U_Cl), and [Co(NH₃)₆]₂[UO₂(CO₃)₃]CO₃ (Co2U_CO₃), which contain differences in the crystalline packing and extended hydrogen bonding networks. We show that these slight changes in the supramolecular assembly and hydrogen bonding networks result in the modification of modes as observed by infrared and Raman spectroscopy. We use density functional theory calculations to assign the vibrational modes and provide an understanding about how uranyl bond perturbation and changes in hydrogen bonding interactions can impact the resulting spectroscopic signals.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 10⁶-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Eu3+ as a luminescence probe in DNA studies: Structural and conformational implications

Lanthanide ions are widely used as luminescent probes for structural studies of various biomolecules, including DNA. Latest developments of circularly polarized luminescence (CPL) methodology further boosted interest to luminescence techniques. However, an effect of the lanthanide probes themselves on the DNA structure and conformation was investigated only partially and not for all lanthanides. In the present work, we performed a detailed spectroscopic study of Eu³⁺ complexes with native double-stranded DNA and compared them to the relevant complexes with single-stranded DNA. We employed infrared (IR), vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopic methods to investigate Eu³⁺ effect on DNA structure and conformational transitions. It was shown that Eu³⁺ ions can induce significant alteration of the native DNA structure at the concentrations often used in luminescence studies. While no DNA denaturation was observed at these metal ion concentrations, significant unstacking of the base pairs and disordering of the sugar-phosphate backbone, partial appearance of the A-form backbone geometry, and DNA transition into condensed ψ-type form took place. Eu³⁺ binding to single-stranded DNA was more pronounced than the binding to double-stranded DNA. We detected the main Eu³⁺ binding sites and determined the metal ion concentration range in which DNA geometry remains largely unaltered. The results obtained in the current study could be used for tuning the luminescence and CPL structural studies of DNA utilizing Eu³⁺ ions as probes.

On the interaction between [Ru(NH3)6]3+ and the G-quadruplex forming thrombin binding aptamer sequence

The interaction between the thrombin binding aptamer (TBA), a G-quadruplex forming DNA sequence, and the electroactive hexaammineruthenium(III) cation has been studied by electrochemical methods and circular dichroism spectroscopy. When TBA is immobilised on a gold surface in a typical aptasensor configuration, the [Ru(NH3)6](3+) cation can be bound to the electrode surface through its interaction with the TBA sequence. This interaction is strong enough to enable the ruthenium complex to remain at the surface when the electrode is immersed in an electrolyte free of [Ru(NH3)6](3+), meaning that the complex does not diffuse back into the solution. A stoichiometry of 2 [Ru(NH3)6](3+) per TBA strand has been determined, indicating that the interaction differs from the conventional, non-specific electrostatic charge compensation, for which a 5 to 1 ratio would be expected between the triply charged cation and the 15 bases sequence. It is shown that this interaction takes place not only at the surface, but also when both TBA and hexaammineruthenium(III) are dissolved in solution. Under such conditions, a similar stoichiometry of 2 [Ru(NH3)6](3+) per TBA strand has been evidenced by two independent methods, namely circular dichroism spectroscopy and differential pulse voltammetry.

Statistical mechanics of columnar DNA assemblies

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA--subject to the earlier found unusual, frustrated pair potential (A.A. Kornyshev, S. Leikin, J. Chem. Phys. 107, 3656 (1997))--onto an exotic, unknown variant of the XY model on a fixed or restructurable lattice. Here, the role of the "spin" is played by the azimuthal orientation of the molecules. We have solved this model using a Hartree-Fock approximation, ground-state calculations, and finite-temperature Monte Carlo simulations. We have found peculiar spin order transitions, which may also be accompanied by positional restructuring, from hexagonal to rhombohedric lattices. Some of these have been experimentally observed in dense columnar aggregates. Note that DNA columnar phases are of great interest in biophysical research, not only because they are a useful in vitro tool for the study of DNA condensation, but also since these structures have been detected in living matter. Within the approximations made, our study provides insight into the statistical mechanics of these systems.

Study of the interaction of hexa-amine cobalt (III) ion with DNA by a resonance light scattering technique and its analytical application

The effect of hexa-amine cobalt cations on the DNA condensation in aqueous solution was investigated by resonance light scattering (RLS). When the relative concentration of hexa-amine cobalt (III) cations to DNA is in the appropriate range, the cations will induce DNA condensation and aggregation, which results in a strong RLS spectrum characterized by a peak at 290.0 nm. The RLS technique is a powerful tool for monitoring DNA condensation and, under optimal conditions, the enhanced RLS intensity at 290.0 nm was proportional to the concentration of DNA in the range 0.01-6.0 microg/mL. Based on this, a sensitive and convenient analysis method for the microdetermination of DNA was established. The detection limit (3 s) of calf thymus DNA by the proposed method is 1.9 ng/mL and few substances interfere in the DNA determination.

Attraction between DNA molecules mediated by multivalent ions

The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counterion and salt ions and different salt concentrations. Computer simulations of the primitive model are used and the shape of the DNA molecules is accurately modeled using different geometrical shapes. We find that multivalent ions induce a significant attraction between the DNA molecules whose strength can be tuned by the averaged valency of the ions. The physical origin of the attraction is traced back either to electrostatics or to entropic contributions. For multivalent counterions and monovalent salt ions, we find a salt-enhanced repulsion effect: the force is first attractive but gets repulsive with increasing salt concentration. Furthermore, we show that the multivalent-ion-induced attraction does not necessarily correlate with DNA overcharging.

Adsorption of monovalent and multivalent cations and anions on DNA molecules

Adsorption of monovalent and multivalent cations and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modeled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modeled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major-groove cationic charge is independent of the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salts. Simulations for larger ion radii, which mimic the effect of ion hydration, indicate an increased adsorbtion of cations in the major groove.

Azimuthal frustration and bundling in columnar DNA aggregates

The interaction between two stiff parallel DNA molecules is discussed using linear Debye-Hückel screening theory with and without inclusion of the dielectric discontinuity at the DNA surface, taking into account the helical symmetry of DNA. The pair potential furthermore includes the amount and distribution of counterions adsorbed on the DNA surface. The interaction does not only depend on the interaxial separation of two DNA molecules, but also on their azimuthal orientation. The optimal mutual azimuthal angle is a function of the DNA-DNA interaxial separation, which leads to azimuthal frustrations in an aggregate. On the basis of the pair potential, the positional and orientational order in columnar B-DNA assemblies in solution is investigated. Phase diagrams are calculated using lattice sums supplemented with the entropic contributions of the counterions in solution. A variety of positionally and azimuthally ordered phases and bundling transitions is predicted, which strongly depend on the counterion adsorption patterns.

Phase behavior of columnar DNA assemblies

The interaction between two stiff parallel DNA molecules depends not only on the distance between their axes but also on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is investigated, on the basis of the electrostatic pair potential that takes into account DNA helical symmetry and the amount and distribution of adsorbed counterions. A phase diagram obtained by lattice sums predicts a variety of positionally and azimuthally ordered phases and bundling transitions strongly depending on the counterion adsorption patterns.

59Co solid-state NMR as a new probe for elucidating metal binding in polynucleotides

Although magnesium fulfills several essential biochemical roles, direct studies on this ion are complicated by its unfavorable spectroscopic characteristics. This contribution explores the possibility of monitoring magnesium-nucleic acid binding via a combination of [Co(NH3)6]3+ as surrogate for [Mg(H2O)6]2+, and of high-resolution solid-state 59Co NMR as a spectroscopic probe. Such strategy quenches fast cationic exchanges between bound and free states, while exploiting the superior NMR properties of the 59Co spin. Experiments on relatively small amounts of tRNA can then discern resonances corresponding to different metal binding environments. These characterizations were assisted by studies on model compounds and by multinuclear 31P-59Co recoupling experiments.

Infrared spectroscopic characterization of the interaction of cationic lipids with plasmid DNA

Fourier transform infrared spectroscopy was used to characterize the interaction of the cationic lipids 1,2-dioleoyl-3-trimethylammonium-propane and dioctadecyldimethylammonium bromide with plasmid DNA. The effect of incorporating the neutral colipids cholesterol and dioleoylphosphatidylethanolamine on this interaction was also examined. Additionally, dynamic and phase analysis light scattering were used to monitor the size and zeta potential of the resulting complexes under conditions similar to the Fourier transform infrared measurements. Results suggest that upon interaction of cationic lipids with DNA, the DNA remains in the B form. Distinct changes in the frequency of several infrared bands arising from the DNA bases, however, suggest perturbation of their hydration upon interaction with cationic lipids. A direct interaction of the lipid ammonium headgroup with and dehydration of the DNA phosphate is observed when DNA is complexed with these lipids. Changes in the apolar regions of the lipid bilayer are minimal, whereas the interfacial regions of the membrane show changes in hydration or molecular packing. Incorporation of helper lipids into the cationic membranes results in increased conformational disorder of the apolar region and further dehydration of the interfacial region. Changes in the hydration of the DNA bases were also observed as the molar ratio of helper lipid in the membranes was increased.

Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine

BACKGROUND

Solvated metal ions are critical for the proper folding and function of RNA. Despite the importance of these ions, the details of specific metal ion-RNA interactions are poorly understood. The crystal structure of a group I intron ribozyme domain characterized several metal-binding sites in the RNA with osmium (III) hexammine bound in the major groove. A corresponding method for locating and characterizing metal-binding sites of RNA in solution is of obvious interest. NMR should be ideal for localizing metal hexammine ions bound to the RNA because of the large concentration of protons around the metal center.

RESULTS

We have solved the solution structure of the P5b stem loop from a group I intron ribozyme bound to a cobalt (III) hexammine ion. The location of the ion is precisely determined by intermolecular nuclear Overhausser effect cross-peaks between the cobalt (III) hexammine protons and both exchangeable and non-exchangeable RNA protons in the major groove. The binding site consists of tandem G-U base pairs in a sequence of four consecutive G residues ending in a GAAA tetraloop, as originally identified in the crystal structure. The edges of the bases in the major groove present an electrostatically negative face and a variety of hydrogen-bond acceptors for the cobalt (III) hexammine ion. The metal ion ligand is bound near the guanosine nucleotides of the adjacent G-U base pairs, where it makes hydrogen bonds with the N7 and carbonyl groups of both guanines. The carbonyl groups of the uracil residues add to the negative surface of the binding pocket, but do not form hydrogen bonds with the hexammine. Additional hydrogen bonds form with other guanine residues of the GGGG sequence. The structure of the binding site does not change significantly on binding the cobalt (III) hexammine. The structure of the complex in solution is very similar to the structure in the crystal.

CONCLUSIONS

The structure presents a picture of how tandem G-U base pairs bind and position metal ions within the RNA major groove. The binding site is performed in the absence of metal ions, and presents a negative pocket in the major groove with a variety of hydrogen-bond acceptors. Because G-U base pairs are such a common motif in RNA sequences, it is possible that this RNA-metal ion interaction is critical in forming large complex RNA structures such as those found in the ribosome and self-splicing introns. This structure was determined using cobalt (III) hexammine as an analog for hexahydrated magnesium, a technique that may be applicable to other RNA sequences. Metal hexammines may prove to be useful general probes for locating RNA metal ion binding sites in solution.

Crystal structure of d(AGGBrCATGCCT): implications for cobalt hexammine binding to DNA

The crystal structure of the DNA decamer d(AGGBrCATGCCT) has been determined to a resolution of 2.0 A and R factor of 19.6%. Crystals of d(AGGBrCATGCCT) were grown in the presence of cobalt hexammine but no cobalt hexammine ions are bound to the DNA structure. This contrasts with the recently determined crystal structure of d(AGGCATGCCT) which has a similar DNA conformation and cobalt hexammine ions bound directly to the DNA. Comparison with the structure of d(AGGCATGCCT) and appreciation of the crystal packing of this sequence leads to an understanding of how cobalt hexammine binding to DNA occurs and its role in determining DNA conformation.

DNA condensation

Recent progress in our understanding of DNA condensation includes the observation of the collapse of single DNA molecules, greater insights into the intermolecular forces driving condensation, the recognition of helix-structure perturbation in condensed DNA, and the increasing recognition of the likely biological consequences of condensation. DNA condensed with cationic liposomes is an efficient agent for the transfection of eukaryotic cells, with considerable potential interest for gene therapy.

An FTIR spectroscopic study of calf-thymus DNA complexation with Al(III) and Ga(III) cations

The interaction of calf-thymus DNA with trivalent Al and Ga cations, in aqueous solution at pH = 6-7 with cation/DNA(P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4 and 1/2 was characterized by Fourier Transform infrared (FTIR) difference spectroscopy. Spectroscopic results show the formation of several types of cation-DNA complexes. At low metal ion concentration (r = 1/80, 1/40), both cations bind mainly to the backbone PO2 group and the guanine N-7 site of the G-C base pairs (chelation). Evidence for cation chelate formation comes from major shifting and intensity increase of the phosphate antisymmetric stretch at 1222 cm-1 and the mainly guanine band at 1717 cm-1. The perturbations of A-T base pairs occur at high cation concentration with major helix destabilization. Evidence for cation binding to A-T bases comes from major spectral changes of the bands at 1663 and 1609 cm-1 related mainly to the thymine and adenine in-plane vibrations. A major reduction of the B-DNA structure occurs in favor of A-DNA upon trivalent cation coordination.

DNA condensation by cobalt hexaammine (III) in alcohol-water mixtures: dielectric constant and other solvent effects

DNA molecules condense into compact structures in the presence of a critical concentration of multivalent cations. To probe the contribution of electrostatic forces to condensation, we used mixtures of water with methanol (MeOH), ethanol (EtOH), and isopropanol (iPrOH) to vary the dielectric constant epsilon from 80 to 50. The condensation of pUC18 plasmids by hexaammine cobalt (III), Co(NH3)(3+)6, was monitored by total intensity and dynamic light scattering, electron microscopy, and CD. The total scattering intensity increased as epsilon went from 80 to 70, and the decreased as epsilon decreased further. Ultraviolet spectrophotometry confirmed that the loss of intensity at low epsilon was not due to the particles' settling out of solution. The rate as well as the extent of condensation increased as epsilon was lowered from 80 to 70, and also depended on the species of alcohol (MeOH < EtOH < iPrOH). The hydrodynamic radii RH of the particles, however, remained roughly the same at 300-350 A and was independent of the species of alcohol. RH increased below epsilon = 70. The critical concentration of Co(NH3)6(3+) required to induce DNA condensation decreased from 21 microM to about 16 microM as the dielectric constant decreased from 80 to 70, and decreased moderately with the nonpolarity of the alcohol. The fraction of DNA charge neutralized at the onset of DNA condensation was calculated by a modification of Manning's two-variable counterion condensation theory to be 0.90 +/- 0.01, independent of epsilon. By electron microscopy we observed that the condensed particles changed from about 93% toroids at epsilon = 80 to 89% rods at epsilon = 70 and 98% rods at epsilon = 65. At epsilon lower than 65, DNA collapsed into a network of multistranded fibers. The morphology of condensed DNA particles, whether toroids, rods, or fibers, was independent of the alcohol species. CD spectra in ethanol-water mixtures indicated that both closed circular and linearized plasmids were in the B conformation when condensed with Co(NH3)6(3+) at epsilon > or = 70, although the closed circular molecules exhibited a weak psi-DNA spectrum. A transition from the B to A form took place between epsilon = 70 and 60, well above the normal dielectric constant of epsilon = 40 for this transition, indicating that ethanol and Co(NH3)6(3+) synergistically promote the B-A transition. We interpret these results to mean that alcohols have both electrostatic and structural effects on DNA, leading to three regimes of condensation. At the lowest alcohol concentrations the B conformation is stable and condensation is relatively slow, allowing time for the packing adjustments necessary to form toroids.(ABSTRACT TRUNCATED AT 400 WORDS)

A comparative study of ATP and GTP complexation with trivalent Al, Ga and Fe cations. Determination of cation binding site and nucleotide conformation by FTIR difference spectroscopy

The interactions of adenosine-5'-triphosphate (Na2H2ATP) and guanosine-5'-triphosphate (Na2H2GTP) with trivalent Al, Ga and Fe cations are investigated in aqueous solution at pH = 6-7 with metal/nucleotide ratios (r) 1/10, 1/2, 1 and 4. Fourier Transform infrared (FTIR) difference spectroscopy is used to characterize the nature of metal cation binding and nucleotide conformational variations, in aqueous solution. Spectroscopic evidences show that at low cation concentration (r = 1/10), metal binding is mainly through the -PO2- and -PO3(2-) groups of the nucleotide moiety (outer-sphere), while at r > 1/10, in addition to direct metal-phosphate binding (chelation), minor metal-base complexes are also formed via indirect metal-NH2 or metal-carbonyl interaction (through H2O). At r = 1, metal macrochelate formation occurs, involving direct cation coordination to phosphate groups and imidazol N-7 atom with an indirect metal-NH2 or metal-carbonyl interaction. At r = 4, polymerization of these metal complexes is observed through nucleotide phosphate chain. The amount of cation/phosphate binding is considerably larger than that of metal/base binding. Evidence for metal-phosphate coordination comes from major spectral changes (shifting and intensity variations) of the alpha-, beta- and gamma-PO2- vibrations in the region 1250-900 cm-1, while metal-base binding is characterized by spectral alterations of the bands at 1700 (guanine carbonyl stretch), 1695 (adenine N-1-H+ mode), 1650-1660 (NH2 bending), 1610-1613 (pyrimidine), 1575 (pyrimidine), 1535-1540 (imidazol), 1470-1480 (imidazol) and 1377 cm-1 (imidazol). The ribose moiety shows C2'-endo/anti conformation for the free ATP and its metal-ATP complexes with an infrared marked band at 821 cm-1. A mixture of both C2'-endo/anti and C3'-endo/anti conformations are occurring for the free GTP and its trivalent metal-complexes with marker bands at 820 and 800 cm-1.

The effect of HCl on the solution structure of calf thymus DNA: a comparative study of DNA denaturation by proton and metal cations using Fourier transform IR difference spectroscopy

The interaction of HCl with calf thymus DNA was investigated in aqueous solution at pH 7-2 with H+/DNA(P) (P:phosphate) molar ratios (r) of 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform (FTIR) difference spectroscopy. Correlations between spectral changes, proton binding mode, DNA denaturation, and conformational variations are established. A comparison was also made between the ir spectra of denaturated DNA, in the presence of proton and Cu ions with similar cation concentrations. The FTIR difference spectroscopic results have shown that at low proton concentrations of r = 1/80 and 1/40 (pH 7-5), no major spectral changes occur for DNA, and the presence of H+ results in an increased base-stacking interaction and helical stability. At higher proton concentrations of r > 1/40, the proton binding to the cytosine and adenine bases begins with major destabilization of the helical duplex. As base protonation progresses, a B to C conformational conversion occurs with major DNA spectral changes. Protonation of guanine bases occurs at a high cation concentration r > 1/2 (pH < 3) with a major increase in the intensity of several DNA in-plane vibrations. Copper ion complexation with DNA exhibits marked similarities with proton at high cation concentrations (r > 1/10), whereas at low metal ion concentrations, copper-PO2 and copper-guanine N-7 bindings are predominant. No major DNA conformational transition was observed on copper ion complexation.