Exclusion of alcohols from spermidine-DNA assemblies: probing the physical basis of preferential hydration

Single Molecular Demonstration of Modulating Charge Inversion of DNA

Charge inversion of DNA is a counterintuitive phenomenon in which the effective charge of DNA switches its sign from negative to positive in the presence of multivalent counterions. The underlying microscopic mechanism is still controversial whether it is driven by a specific chemical affinity or electrostatic ion correlation. It is well known that DNA shows no charge inversion in normal aqueous solution of trivalent counterions though they can induce the conformational compaction of DNA. However, in the same trivalent counterion condition, we demonstrate for the first time the occurrence of DNA charge inversion by decreasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In contrast, the charge inversion of DNA induced by quadrivalent counterions can be canceled out by increasing the dielectric constant of solution. The physical modulation of DNA effective charge in two ways unambiguously demonstrates that charge inversion of DNA is a predominantly electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates by single molecular MT.

Microenvironments created by liquid-liquid phase transition control the dynamic distribution of bacterial division FtsZ protein

The influence of membrane-free microcompartments resulting from crowding-induced liquid/liquid phase separation (LLPS) on the dynamic spatial organization of FtsZ, the main component of the bacterial division machinery, has been studied using several LLPS systems. The GTP-dependent assembly cycle of FtsZ is thought to be crucial for the formation of the septal ring, which is highly regulated in time and space. We found that FtsZ accumulates in one of the phases and/or at the interface, depending on the system composition and on the oligomerization state of the protein. These results were observed both in bulk LLPS and in lipid-stabilized, phase-separated aqueous microdroplets. The visualization of the droplets revealed that both the location and structural arrangement of FtsZ filaments is determined by the nature of the LLPS. Relocation upon depolymerization of the dynamic filaments suggests the protein may shift among microenvironments in response to changes in its association state. The existence of these dynamic compartments driven by phase transitions can alter the local composition and reactivity of FtsZ during its life cycle acting as a nonspecific modulating factor of cell function.

Ionization at a solid-water interface in an applied electric field: Charge regulation

We investigate ionization at a solid-water interface in an applied electric field. We attach an electrode to a dielectric film bearing silanol or carboxyl groups with an areal density Γ₀, where the degree of dissociation α is determined by the proton density in water close to the film. We show how α depends on the density n₀ of NaOH in water and the surface charge density σ_m on the electrode. For σ_m > 0, the protons are expelled away from the film, leading to an increase in α. In particular, in the range 0 < σ_m < eΓ₀, self-regulation occurs to realize α ≅ σ_m/eΓ₀ for n₀ ≪ n_c, where n_c is 0.01 mol/L for silica surfaces and is 2 × 10^-5 mol/L for carboxyl-bearing surfaces. We also examine the charge regulation with decreasing the cell thickness H below the Debye length κ^-1, where a crossover occurs at the Gouy-Chapman length. In particular, when σ_m ∼ eΓ₀ and H ≪ κ^-1, the surface charges remain only partially screened by ions, leading to a nonvanishing electric field in the interior.

Influence of asymmetric depletion of solvents on the electric double layer of charged objects in binary polar solvent mixtures

The ratio of the dipole moment to the volume of solvent is the key factor for asymmetric depletion of solvents.

Changes in free polyamine levels, expression of polyamine biosynthesis genes, and performance of rice cultivars under salt stress: a comparison with responses to drought

Soil salinity affects a large proportion of rural area and limits agricultural productivity. To investigate differential adaptation to soil salinity, we studied salt tolerance of 18 varieties of Oryza sativa using a hydroponic culture system. Based on visual inspection and photosynthetic parameters, cultivars were classified according to their tolerance level. Additionally, biomass parameters were correlated with salt tolerance. Polyamines have frequently been demonstrated to be involved in plant stress responses and therefore soluble leaf polyamines were measured. Under salinity, putrescine (Put) content was unchanged or increased in tolerant, while dropped in sensitive cultivars. Spermidine (Spd) content was unchanged at lower NaCl concentrations in all, while reduced at 100 mM NaCl in sensitive cultivars. Spermine (Spm) content was increased in all cultivars. A comparison with data from 21 cultivars under long-term, moderate drought stress revealed an increase of Spm under both stress conditions. While Spm became the most prominent polyamine under drought, levels of all three polyamines were relatively similar under salt stress. Put levels were reduced under both, drought and salt stress, while changes in Spd were different under drought (decrease) or salt (unchanged) conditions. Regulation of polyamine metabolism at the transcript level during exposure to salinity was studied for genes encoding enzymes involved in the biosynthesis of polyamines and compared to expression under drought stress. Based on expression profiles, investigated genes were divided into generally stress-induced genes (ADC2, SPD/SPM2, SPD/SPM3), one generally stress-repressed gene (ADC1), constitutively expressed genes (CPA1, CPA2, CPA4, SAMDC1, SPD/SPM1), specifically drought-induced genes (SAMDC2, AIH), one specifically drought-repressed gene (CPA3) and one specifically salt-stress repressed gene (SAMDC4), revealing both overlapping and specific stress responses under these conditions.

Evidence for water structuring forces between surfaces

Structured water on apposing surfaces can generate significant energies due to reorganization and displacement of water as the surfaces encounter each other. Force measurements on a multitude of biological structures using the osmotic stress technique have elucidated commonalities that point toward an underlying hydration force. In this review, the forces of two contrasting systems are considered in detail: highly charged DNA and nonpolar, uncharged hydroxypropyl cellulose. Conditions for both net repulsion and attraction, along with the measured exclusion of chemically different solutes from these macromolecular surfaces, are explored and demonstrate common features consistent with a hydration force origin. Specifically, the observed interaction forces can be reduced to the effects of perturbing structured surface water.

Charged colloids in an aqueous mixture with a salt

We calculate the ion and composition distributions around colloid particles in an aqueous mixture, accounting for preferential adsorption, electrostatic interaction, selective solvation among ions and polar molecules, and composition-dependent ionization. On the colloid surface, we predict a precipitation transition induced by a strong preference of hydrophilic ions to water and a prewetting transition between weak and strong adsorption and ionization. These transition lines extend far from the solvent coexistence curve in the plane of the interaction parameter χ (or the temperature) and the average solvent composition. The colloid interaction is drastically altered by these phase transitions on the surface. In particular, the interaction is much amplified on bridging of wetting layers formed above the precipitation line. Such wetting layers can either completely or partially cover the colloid surface depending on the average solvent composition.

Thermodynamics and solvent effects on substrate and cofactor binding in Escherichia coli chromosomal dihydrofolate reductase

Chromosomal dihydrofolate reductase from Escherichia coli catalyzes the reduction of dihydrofolate to tetrahydrofolate using NADPH as a cofactor. The thermodynamics of ligand binding were examined using an isothermal titration calorimetry approach. Using buffers with different heats of ionization, zero to a small, fractional proton release was observed for dihydrofolate binding, while a proton was released upon NADP(+) binding. The role of water in binding was additionally monitored using a number of different osmolytes. Binding of NADP(+) is accompanied by the net release of ∼5-24 water molecules, with a dependence on the identity of the osmolyte. In contrast, binding of dihydrofolate is weakened in the presence of osmolytes, consistent with "water uptake". Different effects are observed depending on the identity of the osmolyte. The net uptake of water upon dihydrofolate binding was previously observed in the nonhomologous R67-encoded dihydrofolate reductase (dfrB or type II enzyme) [Chopra, S., et al. (2008) J. Biol. Chem. 283, 4690-4698]. As R67 dihydrofolate reductase possesses a nonhomologous sequence and forms a tetrameric structure with a single active site pore, the observation of weaker DHF binding in the presence of osmolytes in both enzymes implicates cosolvent effects on free dihydrofolate. Consistent with this analysis, stopped flow experiments find betaine mostly affects DHF binding via changes in k(on), while betaine mostly affects NADPH binding via changes in k(off). Finally, nonadditive enthalpy terms when binary and ternary cofactor binding events are compared suggest the presence of long-lived conformational transitions that are not included in a simple thermodynamic cycle.

Cation charge dependence of the forces driving DNA assembly

Understanding the strength and specificity of interactions among biologically important macromolecules that control cellular functions requires quantitative knowledge of intermolecular forces. Controlled DNA condensation and assembly are particularly critical for biology, with separate repulsive and attractive intermolecular forces determining the extent of DNA compaction. How these forces depend on the charge of the condensing ion has not been determined, but such knowledge is fundamental for understanding the basis of DNA-DNA interactions. Here, we measure DNA force-distance curves for a homologous set of arginine peptides. All forces are well fit as the sum of two exponentials with 2.4- and 4.8-Å decay lengths. The shorter-decay-length force is always repulsive, with an amplitude that varies slightly with length or charge. The longer-decay-length force varies strongly with cation charge, changing from repulsion with Arg¹ to attraction with Arg². Force curves for a series of homologous polyamines and the heterogeneous protein protamine are quite similar, demonstrating the universality of these forces for DNA assembly. Repulsive amplitudes of the shorter-decay-length force are species-dependent but nearly independent of charge within each species. A striking observation was that the attractive force amplitudes for all samples collapse to a single curve, varying linearly with the inverse of the cation charge.

DNA condensations on mica surfaces induced collaboratively by alcohol and hexammine cobalt

We performed systematic studies of λ-DNA condensation on mica surfaces induced by alcohol and hexammine cobalt (III) [Co(NH(3))(6)(3+)] using atomic force microscopy (AFM). The critical condensation concentration for [Co(NH(3))(6)(3+)] was found to be about 10 microM; the DNA molecules extended freely on mica when the concentration was below the critical value. The morphology of condensed DNA became more compact with increasing concentration. At about 500 microM [Co(NH(3))(6)(3+)] concentration, no condensation patterns could be observed due to charge inversion of the compact structures resulting in failure of adhesion to the positively charged surfaces. The critical concentration for alcohol was about 15% (v/v). At this concentration, a few intramolecular loops could be observed in the AFM images. With increasing ethanol concentration the condensation pattern became more complicated ranging from flower-like to pancake-like. When the solution contained both alcohol and hexammine cobalt (III), DNA condensation patterns could be observed even when the concentrations of the two condensation agents were lower than their critical values. We observed this phenomenon by adding mixtures of 10% alcohol and 8 microM hexammine cobalt (III) to DNA solutions. The condensation patterns were more compact than those of the condensation agents separately. Typical toroids were found at an appropriate alcohol and hexammine cobalt (III) concentration. The collaborative condensation phenomenon was analyzed by electrostatic interaction and charge neutralization.

Precipitation in aqueous mixtures with addition of a strongly hydrophilic or hydrophobic solute

We examine phase separation in aqueous mixtures due to preferential solvation with a low-density solute (hydrophilic ions or hydrophobic particles). For hydrophilic ions, preferential solvation can stabilize water domains enriched with ions. This precipitation occurs above a critical solute density n(p) in wide ranges of the temperature and the average composition, where the mixture solvent would be in a one-phase state without solute. The volume fraction of precipitated domains tends to zero as the average solute density n is decreased to np or as the interaction parameter χ is decreased to a critical value χ(p). If we start with one-phase states with n>n(p) or χ>χ(p), precipitation proceeds via homogeneous nucleation or via heterogeneous nucleation, for example, around suspended colloids. In the latter case, colloid particles are wrapped by thick wetting layers. We also predict a first-order prewetting transition for n or χ slightly below np or χ(p) for neutral colloids.

Measuring the interaction of urea and protein-stabilizing osmolytes with the nonpolar surface of hydroxypropylcellulose

The interaction of urea and several naturally occurring protein-stabilizing osmolytes, glycerol, sorbitol, glycine betaine, trimethylamine oxide (TMAO), and proline, with condensed arrays of a hydrophobically modified polysaccharide, hydroxypropylcellulose (HPC), has been inferred from the effect of these solutes on the forces acting between HPC polymers. Urea interacts only very weakly. The protein-stabilizing osmolytes are strongly excluded. The observed energies indicate that the exclusion of the protein-stabilizing osmolytes from protein hydrophobic side chains would add significantly to protein stability. The temperature dependence of exclusion indicates a significant contribution of enthalpy to the interaction energy in contrast to expectations from "molecular crowding" theories based on steric repulsion. The dependence of exclusion on the distance between HPC polymers rather indicates that perturbations of water structuring or hydration forces underlie exclusion.

Electrostatic exclusion of neutral solutes from condensed DNA and other charged phases

Motivated by experiments on condensed DNA phases in binary mixtures of water and a low-dielectric solute, we develop a theory for the electrostatic contribution to solute exclusion from a highly charged phase, within the continuum approximation of the medium. Because the electric field is maximum at the surface of each ion, the electrostatic energy is dominated by the Born energy; interactions between charges are of secondary importance. Neglecting interactions and considering only the competition between the Born energy and the free energy of mixing, we predict that low dielectric solutes are excluded from condensed DNA phases in water-cosolvent mixtures. This suggests that the traditional continuum electrostatic approach of modeling binary mixtures with a uniform dielectric constant needs to be modified. The linking of solute exclusion to solute dielectric properties also suggests a mechanism for predicting the electrostatic contribution to preferential hydration of polar and charged surfaces.

Modulation of psoralen DNA crosslinking kinetics associated with a triplex-forming oligonucleotide

A triplex-forming oligonucleotide (TFO), HPRT3, conjugated to a psoralen derivative, was designed to target a psoralen reaction site within the HPRT gene. HPRT3 bound with high affinity to a synthetic duplex target sequence. At a uniform UVA radiation dose, the ratio of psoralen monoadducts (MA) to interstrand crosslinks decreased and inverted with increasing TFO concentration. As the TFO concentration increased from 10 nm to 10 microm, the efficiency of psoralen MA formation remained relatively constant but the efficiency of interstrand crosslink formation increased several-fold. Neither shortening the TFO to reduce its dissociation constant nor altering the DNA sequences flanking the TFO binding site altered the concentration dependence of MA and crosslink yields. The psoralen photokinetics associated with 10 nm HPRT3 converted to those associated with 10 microm HPRT3 with the addition of other unrelated TFOs at 10 microm that do not specifically interact with the HPRT3 target sequence. Glycerol at concentrations of 0.5% (vol/vol) or higher also mimicked high TFO concentrations in enhancing crosslink formation. These results demonstrate that while psoralen may be targeted to react at a particular sequence by TFOs, photoreactivity associated with triplex formation is also modulated by sequence-independent factors that may affect the local macromolecular environment.

Compatible solute influence on nucleic acids: many questions but few answers

Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications.

Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics.

Attractive forces between cation condensed DNA double helices

By combining single-molecule magnetic tweezers and osmotic stress on DNA assemblies, we separate attractive and repulsive components of the total intermolecular interaction between multivalent cation condensed DNA. Based on measurements of several different cations, we identify two invariant properties of multivalent cation-mediated DNA interactions: repulsive forces decay exponentially with a 2.3 +/- 0.1 A characteristic decay length and the attractive component of the free energy is always 2.3 +/- 0.2 times larger than the repulsive component of the free energy at force-balance equilibrium. These empirical constraints are not consistent with current theories that attribute DNA-DNA attractions to a correlated lattice of counterions. The empirical constraints are consistent with theories for Debye-Hückel interactions between helical line charges and with the order-parameter formalism for hydration forces. Each of these theories posits exponentially decaying attractions and, if we assume this form, our measurements indicate a cation-independent, 4.8 +/- 0.5 A characteristic decay length for intermolecular attractions between condensed DNA molecules.

Molecular crowding effects on structure and stability of DNA

Living cells contain a variety of biomolecules including nucleic acids, proteins, polysaccharides, and metabolites as well as other soluble and insoluble components. These biomolecules occupy a significant fraction (20-40%) of the cellular volume. The total concentration of biomolecules reaches 400gL(-1), leading to a crowded intracellular environment referred to as molecular crowding. Therefore, an understanding of the effects of molecular crowding conditions on biomolecules is important to broad research fields such as biochemical, medical, and pharmaceutical sciences. In this review, we describe molecular conditions in the cytoplasm and nucleus, which are totally different from in vitro conditions, and then show the biochemical and biophysical consequences of molecular crowding. Finally, we discuss the effect of molecular crowding on the structure, stability, and function of nucleic acids and the significance of molecular crowding in biotechnology and nanotechnology.

Osmotically induced helix-coil transition in poly(glutamic acid)

Protein folding and conformational changes are influenced by protein-water interactions and, as such, the energetics of protein function are necessarily linked to water activity. Here, we have chosen the helix-coil transition in poly(glutamic acid) as a model system to investigate the importance of hydration to protein structure by using the osmotic stress method combined with circular dichroism spectroscopy. Osmotic stress is applied using poly(ethylene glycol), molecular weight of 400, as the osmolyte. The energetics of the helix-coil transition under applied osmotic stress allows us to calculate the change in the number of preferentially included water molecules per residue accompanying the thermally induced conformational change. We find that osmotic stress raises the helix-coil transition temperature by favoring the more compact alpha-helical state over the more hydrated coil state. The contribution of other forces to alpha-helix stability also are explored by varying pH and studying a random copolymer, poly(glutamic acid-r-alanine). In this article, we clearly show the influence of osmotic pressure on the peptide folding equilibrium. Our results suggest that to study protein folding in vitro, the osmotic pressure, in addition to pH and salt concentration, should be controlled to better approximate the crowded environment inside cells.

Protein structure and hydration probed by SANS and osmotic stress

Interactions governing protein folding, stability, recognition, and activity are mediated by hydration. Here, we use small-angle neutron scattering coupled with osmotic stress to investigate the hydration of two proteins, lysozyme and guanylate kinase (GK), in the presence of solutes. By taking advantage of the neutron contrast variation that occurs upon addition of these solutes, the number of protein-associated (solute-excluded) water molecules can be estimated from changes in both the zero-angle scattering intensity and the radius of gyration. Poly(ethylene glycol) exclusion varies with molecular weight. This sensitivity can be exploited to probe structural features such as the large internal GK cavity. For GK, small-angle neutron scattering is complemented by isothermal titration calorimetry with osmotic stress to also measure hydration changes accompanying ligand binding. These results provide a framework for studying other biomolecular systems and assemblies using neutron scattering together with osmotic stress.

A balancing act between net uptake of water during dihydrofolate binding and net release of water upon NADPH binding in R67 dihydrofolate reductase

R67 dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate using NADPH as a cofactor. This enzyme is a homotetramer possessing 222 symmetry, and a single active site pore traverses the length of the protein. A promiscuous binding surface can accommodate either DHF or NADPH, thus two nonproductive complexes can form (2NADPH or 2DHF) as well as a productive complex (NADPH.DHF). The role of water in binding was monitored using a number of different osmolytes. From isothermal titration calorimetry (ITC) studies, binding of NADPH is accompanied by the net release of 38 water molecules. In contrast, from both steady state kinetics and ITC studies, binding of DHF is accompanied by the net uptake of water. Although different osmolytes have similar effects on NADPH binding, variable results are observed when DHF binding is probed. Sensitivity to water activity can also be probed by an in vivo selection using the antibacterial drug, trimethoprim, where the water content of the media is decreased by increasing concentrations of sorbitol. The ability of wild type and mutant clones of R67 DHFR to allow host Escherichia coli to grow in the presence of trimethoprim plus added sorbitol parallels the catalytic efficiency of the DHFR clones, indicating water content strongly correlates with the in vivo function of R67 DHFR.

Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA Binding of the restriction endonuclease BamHI

Using the osmotic stress technique together with a self-cleavage assay we measure directly differences in sequestered water between specific and nonspecific DNA-BamHI complexes as well as the numbers of water molecules released coupled to specific complex formation. The difference between specific and nonspecific binding free energy of the BamHI scales linearly with solute osmolal concentration for seven neutral solutes used to set water activity. The observed osmotic dependence indicates that the nonspecific DNA-BamHI complex sequesters some 120-150 more water molecules than the specific complex. The weak sensitivity of the difference in number of waters to the solute identity suggests that these waters are sterically inaccessible to solutes. This result is in close agreement with differences in the structures determined by x-ray crystallography. We demonstrate additionally that when the same solutes that were used in competition experiments are used to probe changes accompanying the binding of free BamHI to its specific DNA sequence, the measured number of water molecules released in the binding process is strikingly solute-dependent (with up to 10-fold difference between solutes). This result is expected for reactions resulting in a large change in a surface exposed area.

Temperature effects on threshold counterion concentration to induce aggregation of fd virus

We seek to elucidate the dominant mechanism of attractive interaction between like-charged biopolymers by measuring the temperature dependence of the critical divalent counterion concentration (Cc) for the aggregation of fd viruses. A decrease in either temperature or the dieletric constant alone causes a decrease in Cc, providing evidence for the Wigner crystal model. Surprisingly, the effects of these two parameters can be combined so that Cc is expressed as a function of a single parameter: the Bjerrum length. Cc decreases exponentially as the Bjerrum length increases, suggesting that an energetic balance between the entropic effect of counterions and the counterion mediated attractive interaction gives rise to the onset of bundle formation.

Effect of organic cosolvents on the free solution mobility of curved and normal DNA molecules

The free solution mobilities of curved and normal 199-bp DNA fragments have been measured in buffer solutions containing various quantities of the organic cosolvents methanol, ethanol, 2-propanol, 2-methyl-2,4-pentanediol (MPD), ethylene glycol, and ACN, using CE. The curved fragment, taken from the VP1 gene of SV40, contains five unevenly spaced A- and T-tracts in a centrally located "curvature module"; the A- and T-tracts have been mutated to other sequences in the normal 199-bp fragment. The free solution mobility of the curved 199-bp fragment is significantly lower than that of its normal counterpart in aqueous solutions [Stellwagen, E., Lu, Y. J., Stellwagen, N. C., Nucleic Acids Res. 2005, 33, 4425-4432]. The mobilities of both the curved and normal fragments decrease with increasing cosolvent concentration, due to the effect of the cosolvent on the viscosity and dielectric constant of the solution. The mobility differences between the curved and normal 199-bp fragments and the mobility ratios decrease approximately linearly with the increasing mole fraction of cosolvent in the solution. Hence, MPD and other organic cosolvents affect DNA electrophoretic mobility by a common mechanism, most likely the preferential hydration of the DNA surface that occurs in aqueous cosolvents. The gradual loss of the anomalously slow mobility of the curved 199-bp fragment with increasing cosolvent concentration, combined with other data in the literature, suggests that preferential hydration gradually widens the narrow A-tract minor groove, releasing site-bound counterions in the minor groove and shifting the conformation toward that of normal DNA.

Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding sequences

We use the osmotic pressure dependence of dissociation rates and relative binding constants to infer differences in sequestered water among complexes of lambda Cro repressor with varied DNA recognition sequences. For over a 1000-fold change in association constant, the number of water molecules sequestered by non-cognate complexes varies linearly with binding free energy. One extra bound water molecule is coupled with the loss of approximately 150 cal/mol complex in binding free energy. Equivalently, every tenfold decrease in binding constant at constant salt and temperature is associated with eight to nine additional water molecules sequestered in the non-cognate complex. The relative insensitivity of the difference in water molecules to the nature of the osmolyte used to probe the reaction suggests that the water is sterically sequestered. If the previously measured changes in heat capacity for lambda Cro binding to different non-cognate sequences are attributed solely to this change in water, then the heat capacity change per incorporated water is almost the same as the difference between ice and water. The associated changes in enthalpies and entropies, however, indicate that the change in complex structure involves more than a simple incorporation of fixed water molecules that act as adaptors between non-complementary surfaces.

Preferential hydration of DNA: the magnitude and distance dependence of alcohol and polyol interactions

The physical forces that underlie the exclusion of solutes from macromolecular surfaces can be probed in a similar way as the measurement of forces between macromolecules in condensed arrays using the osmotic stress technique and x-ray scattering. We report here the dependence of alcohol exclusion or, equivalently, the preferential hydration of DNA on the spacing between helices in condensed arrays. The actual forces describing exclusion are quite different from the commonly assumed steric crowding coupled with weak binding. For a set of 12 nonpolar alcohols, exclusion is due to repulsive hydration interactions with the charged DNA surface. Exclusion amplitudes do not depend simply on size, but rather on the balance between alkyl carbons and hydroxyl oxygens. Polyols are included at very close spacings. The distance dependence of polyol inclusion, however, is quite different from nonpolar alcohol exclusion, suggesting the underlying mechanism of interaction is different.

Incomplete ion dissociation underlies the weakened attraction between DNA helices at high spermidine concentrations

We have investigated the salt sensitivity of the hexagonal-to-cholesteric phase transition of spermidine-condensed DNA. This transition precedes the resolubilization of precipitated DNA that occurs at high spermidine concentration. The sensitivity of the critical spermidine concentration at the transition point to the anion species and the NaCl concentration indicates that ion pairing of this trivalent ion underlies this unusual transition. Osmotic pressure measurements of spermidine salt solutions are consistent with this interpretation. Spermidine salts are not fully dissociated at higher concentrations. The competition for DNA binding among the fully charged trivalent ion and the lesser charged complex species at higher concentrations significantly weakens attraction between DNA helices in the condensed state. This is contrary to the suggestion that the binding of spermidine at higher concentrations causes DNA overcharging and consequent electrostatic repulsion.

Solutes probe hydration in specific association of cyclodextrin and adamantane

Using microcalorimetry, we follow changes in the association free energy of beta-cyclodextrin (CD) with the hydrophobic part of adamantane carboxylate (AD) due to added salt or polar (net-neutral) solutes that are excluded from the molecular interacting surfaces. Changes in binding constants with solution osmotic pressure (water activity) translate into changes in the preferential hydration upon complex formation. We find that these changes correspond to a release of 15-25 solute-excluding waters upon CD/AD association. Reflecting the preferential interaction of solute with reactants versus products, we find that changes in hydration depend on the type of solute used. All solutes used here result in a large change in the enthalpy of the CD-AD binding reaction. In one class of solutes, the corresponding entropy change is much smaller, while in the other class, the entropy change almost fully compensates the solute-specific enthalpy. For many of the solutes, the number of waters released correlates well with their effect on air-water surface tensions. We corroborate these results using vapor pressure osmometry to probe individually the hydration of reactants and products of association, and we discuss the possible interactions and forces between cosolute and hydrophobic surfaces responsible for different kinds of solute exclusion.

Hydration Forces Underlie the Exclusion of Salts and of Neutral Polar Solutes from Hydroxypropylcellulose

The distance dependence for the preferential exclusion of several salts and neutral solutes from hydroxypropyl cellulose (HPC) has been measured via the effect of these small molecules on the thermodynamic forces between HPC polymers in ordered arrays. The concentration of salts and neutral solutes decreases exponentially as the spacing between apposing nonpolar HPC surfaces decreases. For all solutes, the spatial decay lengths of this exclusion are remarkably similar to those observed between many macromolecules at close spacings where intermolecular forces have been ascribed to the energetics of water structuring. Exclusion magnitudes depend strongly on the nature and size of the particular salt or solute; for the three potassium salts studied, exclusion follows the anionic Hofmeister series. The change in the number of excess waters associated with HPC polymers is independent of solute concentration suggesting that the dominating interactions are between solutes and the hydrated polymer. These findings further confirm the importance of solvation interactions and reveal an unexpected unity of Hofmeister effects, preferential hydration, and hydration forces.

Dielectric control of counterion-induced single-chain folding transition of DNA

In the presence of condensing agents, single chains of giant double-stranded DNA undergo a first-order phase transition between an elongated coil state and a folded compact state. To connect this like-charged attraction phenomenon to counterion condensation, we performed a series of single-chain experiments on aqueous solutions of DNA, where we varied the extent of counterion condensation by varying the relative dielectric constant epsilon(r) from 80 to 170. Single-chain observations of changes in the conformation of giant DNA were performed by transmission electron microscopy and fluorescence microscopy, with tetravalent spermine (SPM(4+)) as a condensing agent. At a fixed dielectric constant, single DNA chains fold into a compact state upon the addition of spermine, whereas at a constant spermine concentration single DNA chains unfold with an increase in epsilon(r). In both cases, the transition is largely discrete at the level of single chains. We found that the critical concentration of spermine necessary to induce the single-chain folding transition increases exponentially as the dielectric constant increases, corresponding to 87-88% of the DNA charge neutralized at the onset of the transition. We also observed that the toroidal morphology of compact DNA partially unfolds when epsilon(r) is increased.