Thermodynamics of DNA condensation caused by mn2+ binding

Interaction between Mn2+ ion and the two forms of DNA duplex (supercoiled and linearized pUC119 DNA) in solution has been examined by isothermal titration calorimetry. Although DNA condensation reaction heat was observed at 323 K, this was not the case at 298 K. DNA condensation was entropically driven and supercoiled DNA was found to be more susceptive. The enthalpy of DNA condensation is estimated 0.42 kJ/mol for both DNA forms. Conversely, the entropy of DNA condensation was 0.13 kJ/mol K for supercoiled DNA, and 0.12 kJ/mol K for linearized DNA. The difference of entropy is attributable to their DNA conformation.     

Thermodynamics of binding cationic detergents to bovine serum albumin

Molar ratio (Γ_a) for binding cetyl trimethyl ammonium bromide (CTAB), myristyl trimethyl ammonium bromide (MTAB), dodecyl trimethyl ammonium bromide (DTAB) and cetyl pyridinium chloride (CPCL) to globular protein bovine serum albumin have been measured by equilibrium dialysis technique under various conditions of pH, ionic strength and temperatures. In all cases binding isotherms are S-shaped and at high concentrations of an amine, Γ_a appears to reach a constant value Γ^m_a, Γ^m_a may vary from 1 to 836 depending upon temperature, nature of amines and other solution parameters. The standard free energy changes (ΔG°) for BSA-amine binding have been calculated using appropriate reference states. The order of ΔG° for various systems is found to be in agreement with the order of the maximum extent of binding Γ^m_a. The effects of chain length of the surfactants on ΔG° and Γ^m_a are found to be irregular. ΔS° and ΔH° for binding reactions are also found to be significant in magnitude. Binding interactions at various pH and ionic strengths do not exhibit regularities in terms of electrostatic effects. All these observations lead to the conclusion that the binding sites of BSA are highly heterogeneous so that binding interactions become irregular in nature. All types of interactions are involved in the binding process so that the mechanism of binding in an individual system is complex in nature. The thermal stability and intrinsic viscosity of bovine serum albumin in the presence of amines have been examined in the light of the binding process.     

Comparative analysis of the electrostatics of the binding of cationic proteins to vesicles: Asymmetric location of anionic phospholipids

The role of electrostatics is studied in the adsorption of cationic proteins to zwitterionic phosphatidylcholine (PC) and anionic PC/phosphatidylglycerol (PG) mixed small unilamellar vesicles (SUVs). For model proteins the interaction is monitored vs. PG content at low ionic strength. The adsorption of lysozyme and myoglobin (isoelectric point, pI 7-11) is investigated in SUVs, along with changes of the fluorescence emission spectra of the cationic proteins, via their adsorption on SUVs. In the Gouy-Chapman formalism, the activity coefficient goes with the square of charge number. Deviations from the ideal model could indicate the asymmetric location of the anionic phospholipid in the bilayer inner leaflet, in mixed zwitterionic/anionic SUVs for both lysozyme- and myoglobin-PC/PG systems, in agreement with experiments and molecular dynamics simulations. Fitted effective SUV charge stays constant. Effective—formal difference increases 0.417 e.u. Effective protein charge increases as PC/PG < PC being greater for myoglobin. The molar free energies of the protein in aqueous and lipid phases increase as PC < PC/PG. Both free-energy changes are greater for myoglobin. Effective interfacial charge stays constant for anionic PC/PG SUVs being greater for myoglobin.     

Surface tension study of cationic gemini surfactants binding to DNA

Binding of cationic gemini surfactants alkanediyl-a-ω-bis(dimethyldodecylammonium bromides) with variable polymethylene spacer length ranging from 2 to 12 methylene groups to DNA in NaBr solution is investigated utilizing the tensiometry method. A simple method is presented for calculating the number of surfactant molecules bound to DNA. The results are evaluated in terms of the gemini surfactant spacer length, showing that gemini molecules with either short spacers (2 methylene groups) or long spacers are most efficiently adsorbed to DNA. A weak adsorption to DNA was found for gemini molecules with a medium spacer length (6 methylene groups in the spacer). The binding properties of cationic gemini surfactants as a function of spacer length are consistent with the results obtained by other experimental methods (dynamic light scattering measurements, fluorescence spectroscopy), indicating identical adsorption behaviour of gemini molecules as a function of the spacer length.      

Electrostatics of DNA complexes with cationic lipid membranes

We present the exact solutions of the linear Poisson-Boltzmann equation for several problems relevant to electrostatics of DNA complexes with cationic lipids. We calculate the electrostatic potential and electrostatic energy for lamellar and inverted hexagonal phases, concentrating on the effects of dielectric boundaries. We compare our results for the complex energy with the known results of numerical solution of the nonlinear Poisson-Boltzmann equation. Using the solution for the lamellar phase, we calculate the compressibility modulus and compare our findings with the experimental data available. Also, we treat charge-charge interactions across, along, and between two low-dielectric membranes. We obtain an estimate for the strength of electrostatic interactions of one-dimensional DNA smectic layers across the lipid membrane. We discuss in the end some aspects of two-dimensional DNA condensation and DNA-DNA attraction in the DNA-lipid lamellar phase in the presence of di- and trivalent cations. We analyze the equilibrium DNA-DNA separations in lamellar complexes using the recently developed theory of electrostatic interactions of DNA helical charge motifs.     

DNA condensation induced by cationic surfactant: a viscosimetry and dynamic light scattering study

The compaction of DNA induced by two simple amphiphiles, cetyltrimethylammonium bromide [CTAB] and dodecyldimethylamine oxide [DDAO], has been investigated by means of combined viscosity and dynamic light scattering measurements, to demonstrate the formation of soluble DNA/surfactant complexes, undergoing a coil-globule transition, upon the increase of the amphiphile concentration. In both of the two systems investigated, the complexation process reaches a maximum for a value of the surfactant to DNA phosphate groups molar ratio of about X = 1. Below this critical concentration, the coil and the globule state coexist in the solution, as clearly shown by the bimodal size distribution obtained from the light scattering intensity correlation functions. Some suggestions are given to support a molecular mechanism responsible for the complex formation, both in the case of a cationic surfactant (CTAB) and of a pH-dependent neutral or cationic amphiphile (DDAO), where the hydrophobic interactions play an important role.     

Synthesis and DNA binding of novel water-soluble cationic methylcobalt porphyrins

Organocobalt derivatives of tetracationic water-soluble porphyrins are difficult to prepare via the typical reductive alkylation of the Co(II)(por) (porH(2) = porphyrin ligand). None have been reported. The problem may arise because the porphyrin core is made relatively electron poor by the positively charged peripheral groups. We have circumvented this problem by using the [Co(III)(NH(3))(5)CH(3)](2+) reagent, which inserts the Co(III)-CH(3) moiety directly into porH(2) in water under basic conditions. The method afforded two new [CH(3)Co(por)](4+) derivatives, [CH(3)CoTMpyP(4)](4+) and [CH(3)CoTMAP](4+), where [TMpyP(4)](4+) and [TMAP](4+) are the coordinated, NH-deprotonated forms of meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin and meso-tetrakis(N,N,N-trimethylaniliniumyl)porphyrin, respectively. The binding of the two new [CH(3)Co(por)](4+) cations to DNA and to the synthetic DNA polymers [poly(dA-dT)](2) and [poly(dG-dC)](2) was studied. Using published criteria by which changes in DNA viscosity and in the visible and CD spectra in the Soret region can be used to assess DNA binding, we conclude that both are outside binders. A large hypochromicity of the Soret bands of the [CH(3)Co(por)](4+) cations observed upon outside binding to DNA may indicate a high degree of self-stacking. The visible absorption and CD spectra of the [CH(3)Co(por)](4+) cations in the presence of 1:1 mixtures of [poly(dA-dT)](2) and [poly(dG-dC)](2) are nearly identical to those with [poly(dA-dT)](2) alone and are very different from those of [poly(dG-dC)](2) alone. Thus, both cations show a high preference for outside binding at AT-rich over GC-rich DNA sites. Upon binding of each of the [CH(3)Co(por)](4+) cations to all of the DNA polymers, the Soret bands exhibit blue shifts, whereas the Soret bands of the corresponding [(H(2)O)(2)Co(por)](5+) cations exhibit red shifts. The blue shifts strongly suggest that the [CH(3)Co(por)](4+) cations, particularly [CH(3)CoTMAP](4+), become five-coordinate forms to some extent on DNA binding; this result is the first good evidence for the presence at equilibrium of five-coordinate CH(3)Co(III)(N(4)) forms in water.     

Specific ion binding to macromolecules: effects of hydrophobicity and ion pairing

Using molecular dynamics simulations in an explicit aqueous solvent, we examine the binding of fluoride versus iodide to a spherical macromolecule with both hydrophobic and positively charged patches. Rationalizing our observations, we divide the ion association interaction into two mechanisms: (1) poorly solvated iodide ions are attracted to hydrophobic surface patches, while (2) the strongly solvated fluoride and to a minor extent also iodide bind via cation-anion interactions. Quantitatively, the binding affinities vary significantly with the accessibility of the charged groups as well as the surface potential; therefore, we expect the ion-macromolecule association to be modulated by the local surface characteristics of the (bio-)macromolecule. The observed cation-anion pairing preference is in excellent agreement with experimental data.     

Role of the spacer of cationic gemini amphiphiles in the condensation of DNA

The condensation of calf thymus DNA into the cholesteric-like psi-phase was observed by circular dichroism in liposome suspensions formulated with specific cationic gemini surfactants. The stereochemistry of the gemini spacer, the presence of specific functional groups, and the covalent link between the headgroups are fundamental issues in the condensation of DNA. Transmission electron microscopy images showed a multilamellar morphology, which corresponds with condensation.     

Thermodynamics of condensation of phthalonitrile with m-phenylenediamine

Conclusions The reaction of phthalonitrile condensation with m-phenylenediamine is thermodynamically allowed at temperatures from 250° to 500°K, and its equilibrium is almost completely shifted toward the formation of the macroheterocycle.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 4, pp. 779–787, April, 1984.     

DNA–DNA electrostatic interactions within cationic lipid/DNA lamellar complexes

We present a simple theoretical analysis of the DNA–DNA electrostatic interactions within charge-neutral lamellar cationic lipid/DNA complexes (lipoplexes). Although always repulsive as a function of the DNA–DNA interaxial distance, the calculated electrostatic force shows a deep minimum for each value of lipid composition corresponding to an equilibrium distance of the system. The excellent agreement between the equilibrium distances predicted by the model and that experimentally observed in charge-neutral complexes as revealed by synchrotron X-ray diffraction, shows that the spatial dimensionality of both the lipids and the DNA may not be a crucial point to capture the essence of the DNA–DNA interactions within charge-neutral lipoplexes.     

The use of capillary electrophoresis with entangled polymer matrix to analyse plasmid DNA and a cationic lipid/cholesterol liposome: DNA complex

Summary A liposome based gene therapeutic product is being developed for the treatment of cystic fibrosis. The product comprises a complex of plasmid DNA and a cationic lipid/cholesterol liposome. Using CE with an entangled polymer matrix, routine separations of linear, supercoiled and open-circle conformers of DNA in plasmid DNA and the liposome complex have been performed. The CE method has been used to support novel quality control and process validation for the manufacture of plasmid DNA and to monitor the degradation of DNA in the liposome complex. Significant features of the method are simple sample preparation and the use of direct UV detection, avoiding the use of potentially mutagenic reagents.     

The interaction between DNA and cationic lipid films at the air-water interface

The interaction between DNA and positively charged dioctadecyldimethylammonium bromide (DODAB) and DODAB/disteroylphosphatidylcholine (DSPC) monolayers at the air-aqueous interface was studied by a combination of the surface film balance and Brewster angle microscopy. In presence of DNA, the Pi-A isotherm of the cationic monolayer shifts to larger mean molecular areas due to the electrostatic interaction with DNA while the typical liquid expanded-liquid condensed phase transition for DODAB monolayers disappear and the monolayer remains to be in the liquid expanded phase. Furthermore, the morphology of the film dramatically changes, where the large dendritic-like condensed aggregates observed for DODAB monolayers vanish. The charge density of the monolayer was varied by using mixed monolayers with the zwitterionic DSPC and no large effect was observed on the interaction with DNA. By modeling the electrostatic interactions with the linearized Poisson-Boltzmann equation using the finite-element method and taking into account the assumption in the dielectric constants of the system, it was possible to corroborate the expansion of the cationic monolayer upon interaction with DNA as well as the fact that DNA does not seem to penetrate into the monolayer.     

DNA condensation induced by a cationic polymer studied by atomic force microscopy and electrophoresis assay

We synthesized a cationic polymer, poly(PEGMA)-4N, which has brush-like chains and four positively charged amino groups at the end of the molecules. DNA condensation induced by poly(PEGMA)-4N was investigated through electrophoresis assay by its ability to retard DNA mobility and to inhibit HindIII enzyme cleavage. The detailed structures of DNA condensates induced by poly(PEGMA)-4N were observed through atomic force microscopy (AFM). Interactions between polymers and DNA are mainly attributed into depletion effect and electrostatic interaction. Positively charged amino groups in poly(PEGMA)-4N interact with DNA through electrostatic interaction, and depletion effect also takes effect because poly(PEGMA)-4N is a flexible polymer. Comparing the contributions that the two interactions gave in DNA condensation process, we found that depletion effect played a major role compared with electrostatic interaction.     

Multiple protonation equilibria in electrostatics of protein-protein binding

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics algorithms with so-called accelerated molecular dynamics algorithms.     

On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations

Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calculations lead to large variations of calculated absolute and relative electrostatic binding free energies. Hence, parametrization of solvation effects based on hydration data, although a necessary condition, is not sufficient to guarantee its transferability to the calculation of binding free energies in solution.     

Robust identification of binding hot spots using continuum electrostatics: application to hen egg-white lysozyme

Binding hot spots, protein regions with high binding affinity, can be identified by using X-ray crystallography or NMR spectroscopy to screen libraries of small organic molecules that tend to cluster at such hot spots. FTMap, a direct computational analogue of the experimental screening approaches, uses 16 different probe molecules for global sampling of the surface of a target protein on a dense grid and evaluates the energy of interaction using an empirical energy function that includes a continuum electrostatic term. Energy evaluation is based on the fast Fourier transform correlation approach, which allows for the sampling of billions of probe positions. The grid sampling is followed by off-grid minimization that uses a more detailed energy expression with a continuum electrostatics term. FTMap identifies the hot spots as consensus clusters formed by overlapping clusters of several probes. The hot spots are ranked on the basis of the number of probe clusters, which predicts their binding propensity. We applied FTMap to nine structures of hen egg-white lysozyme (HEWL), whose hot spots have been extensively studied by both experimental and computational methods. FTMap found the primary hot spot in site C of all nine structures, in spite of conformational differences. In addition, secondary hot spots in sites B and D that are known to be important for the binding of polysaccharide substrates were found. The predicted probe-protein interactions agree well with those seen in the complexes of HEWL with various ligands and also agree with an NMR-based study of HEWL in aqueous solutions of eight organic solvents. We argue that FTMap provides more complete information on the HEWL binding site than previous computational methods and yields fewer false-positive binding locations than the X-ray structures of HEWL from crystals soaked in organic solvents.     

Characterization of the nanostructure of complexes formed by a redox-active cationic lipid and DNA

We report characterization of the nanostructures of complexes formed between the redox-active lipid bis(n-ferrocenylundecyl)dimethylammonium bromide (BFDMA) and DNA using small-angle neutron scattering (SANS) and cryogenic transmission electron microscopy (cryo-TEM). A particular focus was directed to the influence of lipid oxidation state (where reduced BFDMA has a net charge of +1 and oxidized BFDMA has a charge of +3) on the nanostructures of the solution aggregates formed. Complexes were characterized over a range of charge ratios of reduced BFDMA to DNA (1.1:1, 2.75:1, and 4:1) in solutions of 1 mM Li2SO4. For these complexes, a single peak in the SANS data at 1.2 nm(-1) indicated that a nanostructure with a periodicity of 5.2 nm was present, similar to that observed with complexes of the classical lipids DODAB/DOPE and DNA (multilamellar spacing of 7.0 nm). The absence of additional Bragg peaks in all the SANS data indicated that the periodicity did not extend over large distances. Both inverse Fourier transform analysis and form factor fitting suggested formation of a multilamellar vesicle. These results were confirmed by cryo-TEM images in which multilamellar complexes with diameters between 50 and 150 nm were observed with no more than seven lamellae per aggregate. In contrast to complexes of reduced BFDMA and DNA, Bragg peaks were absent in SANS spectra of complexes formed by oxidized BFDMA and DNA at all charge ratios investigated. The low-q behavior of the SANS data obtained using oxidized BFDMA and DNA complexes suggested that large, loose aggregates were formed, consistent with complementary cryo-TEM images showing predominantly loose disordered aggregates. Some highly ordered spongelike and cubic phase nanostructures were also detected in cryo-TEM images. We conclude that control of BFDMA oxidation state can be used to manipulate the nanostructures of lipid-DNA complexes formed using BFDMA.     

Thermodynamics of micellization of multiheaded single-chain cationic surfactants

The energetics of micelle formation of three single-chain cationic surfactants bearing single (h = 1), double (h = 2), and triple (h = 3) trimethylammonium [(+)N(CH(3))(3)] headgroups have been investigated by microcalorimetry. The results were compared with the microcalorimetric data obtained from well-known cationic surfactant, cetyl trimethylammonium bromide (CTAB), bearing a single chain and single headgroup. The critical micellar concentrations (cmc's) and the degrees of counterion dissociation (alpha) of micelles of these surfactants were also determined by conductometry. The cmc and the alpha values increased with the increase in the number of headgroups of the surfactant. The relationship between the cmc of the surfactant in solution and its free energy of micellization (DeltaG(m)) was derived for each surfactant. Exothermic enthalpies of micellization (DeltaH(m)) and positive entropies of micellization (DeltaS(m)) were observed for all the surfactants. Negative DeltaH(m) values increased from CTAB to h = 1 to h = 2 and decreased for h = 3 whereas DeltaS(m) values decreased with increase in the number of headgroups. The DeltaG(m) values progressively became less negative with the increase in the number of headgroups. This implies that micelle formation becomes progressively less favorable as more headgroups are incorporated in the surfactant. From the steady-state fluorescence measurements using pyrene as a probe, the micropolarities sensed by the probe inside various micelles were determined. These studies suggest that the micelles are more hydrated with multiheaded surfactants and the micropolarity of micelles increases with the increase in the number of headgroups.