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

The interaction of the alcohols 2-methyl-2,4-pentanediol (MPD) and 2-propanol and of glycerol with condensed spermidine(3+)-DNA arrays are investigated with direct force measurements using osmotic stress coupled with X-ray scattering. Thermodynamic forces between DNA helices are measured from the dependence of helical interaxial spacings on the osmotic pressure applied by poly(ethylene glycol) solutions in equilibrium with the DNA phase. The sensitivity of these forces to solute concentration can be transformed into a change in the number of excess or deficit solutes or waters in the DNA phase by applying the Gibbs-Duhem equation. The alcohols examined are excluded from the condensed DNA array and strongly affect the osmotic stress force curves. DNA is preferentially hydrated. MPD is significantly more excluded than 2-propanol. The exclusion of these alcohols, however, is not due to a steric repulsion since glycerol that is intermediate in size between MPD and 2-propanol does not observably affect DNA force curves. As the distance between DNA helices varies, the change in the number of excess waters is independent of alcohol concentration for each alcohol. These solutes are acting osmotically on the condensed array. The distance dependence of exclusion indicates that repulsive water structuring forces dominate the interaction of alcohols with the DNA surface. The exclusion measured for these condensed arrays can quantitatively account for the effect of these alcohols on the precipitation of DNA from dilute solution by spermidine(3+).     

The entropically favored osmotic "compression" of sickle cell hemoglobin gels

Contrary to the accurate, hard-sphere depiction of monomeric hemoglobin in solution, sickle cell hemoglobin (HbS) polymerization/gelation requires attention to molecular interactions. From the temperature dependence of the osmotic compressibility of HbS gels, we were able to extract the entropy increase for concentrating HbS in this phase. Normalized per mole of water removed, the entropy increase from gel compression DeltaS(gel) is four times the previously measured DeltaS(trans), for the transition from monomeric HbS solution to HbS gel. The positive entropy change cannot emerge from the assembly of hard spheres but can indicate remodeling of HbS fibers driven by release of ordered water. The fourfold difference in DeltaS(gel) and DeltaS(trans) suggests that the act of initial fiber/gel formation from monomeric solution differs from the process of further polymerization due to tighter packing within the gel phase.     

Helix-specific interactions induce condensation of guanosine four-stranded helices in concentrated salt solutions.

Deoxyguanosine-5'-monophosphate in water self-associates into stable structures, which include liquid-crystalline hexagonal and cholesteric phases. The structural unit is a four-stranded helix, composed of stacked Hoogsteen-bonded guanosine quartets. By using the osmotic stress method, we recently measured the force between helices in KCl solutions up to 2 M. In addition to the long-range electrostatic force, a short-range hydration repulsive contribution was recognized. The hydration repulsion is exponential, and shows a decay length independent from the ionic strength of the solution. Here, we report that more concentrated KCl solutions cause condensation of the guanosine helix in a hexagonal phase with constant equilibrium separation of approximately 7 A between helix surfaces. Long-range attraction, which induces the self-assembly, and short-range repulsion, which prevents the contact between the helices, are implied. By using osmotic stress, the force needed to push helices closer from the spontaneously assumed position has been measured. The attractive force was then estimated as a difference between the net force and the repulsive contribution, revealing an exponential decay length about two times larger than that of the short-range repulsion. The agreement with the helix interaction theory introduced recently by Kornyshev and Leikin (Kornyshev, A. A., and S. Leikin, 1997. Theory of interaction between helical molecules. J. Phys. Chem. 107:3656-3674) suggests that the repulsive and attractive forces originate from helix-specific interactions.     

Ion disturbance and clustering in the NaCl water solutions

Ion clustering and the solvation properties in the NaCl solutions are explored by molecular dynamics simulations with several popular force fields. The existence of ions has a negligible disturbance to the hydrogen bond structures and rotational mobility of water beyond the first ion solvation shells, which is suggested by the local hydrogen bond structures and the rotation times of water. The potential of mean force (PMF) of ion pair in the dilute solution presents a consistent view with the populations of ion clusters in the electrolyte solutions. The aggregation level of ions is sensitive to the force field used in the simulations. The ion-ion interaction potential plays an important role in the forming of the contact ion pair. The entropy of water increases as the ion pair approaches each other and the association of ion pair is driven by the increment of water entropy according to the results from the selected force fields. The kinetic transition from the single solvent separated state to the contact ion pair is controlled by the enthalpy loss of solution.

Measurement of intercolumnar forces between parallel guanosine four-stranded helices.

The deoxyguanosine-5'-monophosphate in aqueous solution self-associates into stable structures, which include hexagonal and cholesteric columnar phases. The structural unit is a four-stranded helix, composed of a stacked array of Hoogsteen-bonded guanosine quartets. We have measured by osmotic stress method the force per unit length versus interaxial distance between helices in the hexagonal phase under various ionic conditions. Two contributions have been recognized: the first one is purely electrostatic, is effective at large distances, and shows a strong dependence on the salt concentration of the solution. The second contribution is short range, dominates at interaxial separations smaller than about 30-32 A, and rises steeply as the columns approach each other, preventing the coalescence of the helices. This repulsion has an exponential nature and shows a magnitude and a decay length insensitive to the ionic strength of the medium. Because these features are distinctive of the hydration force detected between phospholipid bilayers or between several linear macromolecules (DNA, polysaccharides, collagen), we conclude that the dominant force experienced by deoxyguanosine helices approaching contact is hydration repulsion. The observed decay length of about 0.7 A has been rationalized to emerge from the coupling between the 3-A decay length of water solvent and the helically ordered structure of the hydrophilic groups on the opposing surfaces. The present results agree with recent measurements, also showing the dependence of the hydration force decay on the structure of interacting surfaces and confirm the correlations between force and structure.     

Ion-mediated nucleic acid helix-helix interactions

Salt ions are essential for the folding of nucleic acids. We use the tightly bound ion (TBI) model, which can account for the correlations and fluctuations for the ions bound to the nucleic acids, to investigate the electrostatic free-energy landscape for two parallel nucleic acid helices in the solution of added salt. The theory is based on realistic atomic structures of the helices. In monovalent salt, the helices are predicted to repel each other. For divalent salt, while the mean-field Poisson-Boltzmann theory predicts only the repulsion, the TBI theory predicts an effective attraction between the helices. The helices are predicted to be stabilized at an interhelix distance approximately 26-36 A, and the strength of the attractive force can reach -0.37 k(B)T/bp for helix length in the range of 9-12 bp. Both the stable helix-helix distance and the strength of the attraction are strongly dependent on the salt concentration and ion size. With the increase of the salt concentration, the helix-helix attraction becomes stronger and the most stable helix-helix separation distance becomes smaller. For divalent ions, at very high ion concentration, further addition of ions leads to the weakening of the attraction. Smaller ion size causes stronger helix-helix attraction and stabilizes the helices at a shorter distance. In addition, the TBI model shows that a decrease in the solvent dielectric constant would enhance the ion-mediated attraction. The theoretical findings from the TBI theory agree with the experimental measurements on the osmotic pressure of DNA array as well as the results from the computer simulations.     

Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition

Measurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard-core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.     

Electrostatic free energy landscapes for nucleic acid helix assembly

Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na⁺ and Mg²⁺ play distinctive roles in helix–helix assembly. High [Na⁺] (>0.3 M) causes a reduced helix–helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg²⁺ of concentration >1 mM is predicted to induce helix–helix attraction and results in a more compact and ordered helix–helix packing. Mg²⁺ is much more efficient in causing nucleic acid compaction. In addition, the free energy landscape shows that the tethering loops between the helices also play a significant role. A flexible loop, such as a neutral loop or a polynucleotide loop in high salt concentration, enhances the close approach of the helices in order to gain the loop entropy. On the other hand, a rigid loop, such as a polynucleotide loop in low salt concentration, tends to de-compact the helices. Therefore, a polynucleotide loop significantly enhances the sharpness of the ion-induced compaction transition. Moreover, we find that a larger number of helices in the system or a smaller radius of the divalent ions can cause a more abrupt compaction transition and a more compact state at high ion concentration, and the ion size effect becomes more pronounced as the number of helices is increased.     

Stretching of single collapsed DNA molecules

The elastic response of single plasmid and lambda phage DNA molecules was probed using optical tweezers at concentrations of trivalent cations that provoked DNA condensation in bulk. For uncondensed plasmids, the persistence length, P, decreased with increasing spermidine concentration before reaching a limiting value 40 nm. When condensed plasmids were stretched, two types of behavior were observed: a stick-release pattern and a plateau at approximately 20 pN. These behaviors are attributed to unpacking from a condensed structure, such as coiled DNA. Similarly, condensing concentrations of hexaammine cobalt(III) (CoHex) and spermidine induced extensive changes in the low and high force elasticity of lambda DNA. The high force (5-15 pN) entropic elasticity showed worm-like chain (WLC) behavior, with P two- to fivefold lower than in low monovalent salt. At lower forces, a 14-pN plateau abruptly appeared. This corresponds to an intramolecular attraction of 0.083-0.33 kT/bp, consistent with osmotic stress measurements in bulk condensed DNA. The intramolecular attractive force with CoHex is larger than with spermidine, consistent with the greater efficiency with which CoHex condenses DNA in bulk. The transition from WLC behavior to condensation occurs at an extension about 85% of the contour length, permitting looping and nucleation of condensation. Approximately half as many base pairs are required to nucleate collapse in a stretched chain when CoHex is the condensing agent.     

The double helix is dehydrated: evidence from the hydrolysis of acridinium ester-labeled probes

A highly chemiluminescent reporter molecule, acridinium ester (AE), was tethered to single-stranded oligonucleotide probes and hybridized to complementary as well as mismatched target sequences. When tethered to single-stranded probes, AE was readily hydrolyzed by water or hydroxide ion. In contrast, when hybridized to a complementary target, hydrolysis of the AE probe was markedly inhibited. Mismatches near AE eliminated the ability of the double helix to strongly inhibit AE hydrolysis. To establish the molecular basis for these remarkable hydrolysis properties of AE-labeled probes, the binding and hydrolysis mechanisms of AE-labeled probes were examined. When tethered to single- or double-stranded nucleic acids, hydrolysis of AE was found to proceed by generalized base catalysis in which a base abstracts a proton from water and the resulting hydroxide ion then hydrolyzes AE. Analysis of the hydrolysis rates of AE bound to DNA revealed that AE binds the minor groove of DNA and that its hydrolysis is inhibited by low water activity within the minor groove of the helix. Depending upon the sequence of the DNA, the water activity of the minor groove was estimated to be at least 2-4-fold lower than bulk solution. Hydrolysis measurements of AE tethered to RNA as well as RNA/DNA hybrids argued that the grooves of these double helices are also dehydrated relative to bulk solution. Remarkably, mismatched bases, regardless of their structure or sequence context, enhanced hydrolysis of AE by inducing hydration of the double helix that spread approximately five base pairs on either side of the mismatch.     

Electrostatic effects on the stability of condensed DNA in the presence of divalent cations.

Cylindrical cell model Poisson-Boltzmann (P-B) calculations are used to evaluate the electrostatic contributions to the relative stability of various DNA conformations (A, B, C, Z, and single-stranded (ss) with charge spacings of 3.38 and 4.2 A) as a function of interhelix distance in a concentrated solution of divalent cations. The divalent ion concentration was set at 100 mM, to compare with our earlier reports of spectroscopic and calorimetric experiments, which demonstrate substantial disruption of B-DNA geometry. Monovalent cations neutralize the DNA phosphates in two ways, corresponding to different experimental situations: 1) There is no significant contribution to the ionic strength from the neutralizing cations, corresponding to DNA condensation from dilute solution and to osmotic stress experiments in which DNA segments are brought into close proximity to each other in the presence of a large excess of buffer. 2) The solution is uniformly concentrated in DNA, so that the neutralizing cations add significantly to those in the buffer at close DNA packing. In case 1), conformations with lower charge density (Z and ssDNA) have markedly lower electrostatic free energies than B-DNA as the DNA molecules approach closely, due largely to ionic entropy. If the divalent cations bind preferentially to single-stranded DNA or a distorted form of B-DNA, as is the case with transition metals, the base pairing and stacking free energies that stabilize the double helix against electrostatic denaturation may be overcome. Strong binding to the bases is favored by the high concentration of divalent cations at the DNA surface arising from the large negative surface potential; the surface concentration increases sharply as the interhelical distance decreases. In case 2), the concentration of neutralizing monovalent cations becomes very large and the electrostatic free energy difference between secondary structures becomes small as the interhelical spacing decreases. Such high ionic concentrations will be expected to modify the stability of DNA by changing water activity as well as by screening electrostatic interactions. This may be the root of the decreased thermal stability of DNA in the presence of high concentrations of magnesium ions.     

Water stress induced by PEG decreases the maximum growth pressure of the roots of pea seedlings

Roots of plants growing in dry soil often experience large mechanical impedance because the decreased soil water content is associated with increased in soil strength. The combined effect of mechanical impedance and water stress hinders the establishment of seedlings in many soils, but little is known about the interaction between these two stresses. A method has been designed that, for the first time, measured the maximum axial force exerted by a root growing under controlled water stress. Using this technique the axial force exerted by a pea radicle was measured using a shear beam, while the seedling was suspended in an aerate solution of polyethylene glycol 20 000 at osmotic potentials between 0 and -0.45 MPa. The maximum growth force was then divided by the cross-sectional area of the root to give the maximum axial growth pressure. The value of maximum axial growth pressure decreased linearly from 0.66 and 0.35 MPa as the osmotic potentials of the solution of PEG decreased from 0 to -0.45 MPa. In dry soil, therefore, the maximum strength of soil that a root can penetrate is decreased because of the decrease in maximum growth pressure. The elongation rates of unimpeded roots were similar whether the roots were subject to either a matric potential in soil or to an osmotic potential in a solution of PEG.Key words: Pisum sativum L, pea, mechanical impedance, axial growth pressure, water stress, PEG 20 000.      

Effect of cations on purine.purine.pyrimidine triple helix formation in mixed-valence salt solutions.

The effect of various monovalent, divalent and oligovalent cations on the reaction of triplex formation by GT and AG motif triplex-forming oligonucleotides, designed to bind to biologically relevant polypurine-polypyrimidine sequences occurring in the promoters of the murine Ki-ras and human bcr genes, has been investigated by means of electrophoresis mobility shift assays (EMSA) and DNase I footprinting experiments. We found that in the presence of 10 mm MgCl2 the triple helices were progressively destabilized by adding increasing amounts of NaCl, from 20 to 140 mm, to the solution. We also observed that, while the total monovalent-ion concentration was constant at 100 mm, the exchange of sodium with potassium, but not lithium, results in a further destabilization of the triple helices, due to self-association equilibria involving the G-rich triplex-forming oligonucleotides. Potassium was found to destabilize triplex DNA even when the triple helices are preformed in the absence of K+. However, footprinting experiments also showed that the inhibitory effect of K+ on triplex DNA is partially compensated for by millimolar amounts of divalent transition metal ions such as Mn2+ and Ni2+, which upon coordinating to N7 of guanine are expected to enhance hydrogen-bond formation between the target and the third strand, and to reduce the assembly in quadruple structures of G-rich triplex-forming oligonucleotides. Triplex enhancement in the presence of potassium was also observed, but to a lesser extent, when spermine was added to the reaction mixture. Here, the ion effect on triplex DNA is rationalized in terms of competition among the different valence cations to bind to triplex DNA, and differential cation stabilization of unusual quadruplex structures formed by the triplex-forming oligonucleotides.     

用渗透胁迫鉴定小麦种子萌发期抗旱性的方法分析

本以聚乙二醇(PEG)-6000、甘露醇和蔗糖作为渗透剂模拟水分胁迫,胁迫溶液渗透势范围在-0．25MPa到-1．50MPa,分析适于进行小麦种子水分胁迫萌发试验的条件,以鉴定小麦萌发期的抗旱性。结果表明,蔗糖溶液易诱发霉茵,胚芽不能正常生长。渗透势为-0．25MPa的PEG-6000及-0．50MPa的甘露醇胁迫已经显抑制了胚芽伸长;-0．50MPa的PEG-6000及-1．00MPa的甘露醇显抑制种子萌发,随着胁迫强度增加,种子相对发芽率及胚芽长度减小,主要是因为渗透胁迫降低了种子吸水速度,胚芽的相对含水量和渗透势均低。在渗透势相同的胁迫条件下,PEG-6000对小麦种子萌发各项检测值的抑制作用均大于甘露醇。如果目的是通过鉴定小麦种子在高渗溶液中的萌发情况,评价萌发期的抗旱性。选用-0．50MPa的PEG-6000或-1．00MPa的甘露醇较为理想,若同时考虑降低试验成本,则应首选-0．50MPa的PEG-6000。     

水分胁迫下小麦幼苗呼吸代谢的改变

水分胁迫下小麦幼苗叶和根的呼吸速率变化模式不同:叶片呼吸在胁迫初期升高,然后随相对含水量进一步递减而急剧下降;根的呼吸速率随相对含水量降低成指数下降。自然干旱和PEG渗透胁迫下得到的结果基本一致。小麦叶片在轻度水分胁迫下呼吸上升与磷酸化解偶联有关。水分胁迫也引起呼吸代谢途径的改变。轻度水分胁迫使叶片呼吸速率升高时,EMP途径运行程度稍有上升;增加的呼吸主要通过TCAC;线粒体呼吸中通过细胞色素主链的电子流量增加,抗氰交替途径的相对运行程度下降。当水分胁迫降低根呼吸速率时,EMP和TCAC的运行程度明显降低;细胞色素途径的运行程度也下降,但仍传递大约一半的呼吸电子流。     

Molecular recognition. I. Automatic identification of topographic surface features

The phenomenon of molecular recognition depends strongly on surface complementarity between associating molecular units, analogous to the assembly of a three-dimensional jigsaw puzzle. The driving force for association is solvent entropy, which increases when protrusions of the irregular surface of one subunit fit snugly into invaginations of the other, squeezing out intervening water. To model this process, an algorithm is presented that automatically finds the prominent topographic surface features of rigid α-helices in proteins of known structure. When the algorithm was applied to two interacting helices from flavodoxin, only a small number of such features were found, and they accounted for the observed complementarity. Using this algorithm, molecular docking can be reduced to a tractable problem by a docking strategy based on exhaustive trial of combinations of surface features.     

Folding transition into a loosely collapsed state in plasmid DNA as revealed by single-molecule observation

The conformational transition of a plasmid DNA, pGEG.GL3 (12.5 kbp, circular), induced by spermine(4+) was studied through the observation of individual DNA by fluorescence microscopy. We deduced the change in the hydrodynamic radius R(H) from an analysis of the Brownian motion of single DNA molecules. R(H) decreases in a continuous manner with an increase in spermine(4+), in contrast to the large discrete on/off change for long linear DNA. Just after the transition to the collapsed state, a small number of DNA molecules tend to form an assembly, which disperses in the bulk solution without precipitation.     

Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching

When a single molecule of double-stranded DNA is stretched beyond its B-form contour length, the measured force shows a highly cooperative overstretching transition. We have measured the force at which this transition occurs as a function of temperature. To do this, single molecules of DNA were captured between two polystyrene beads in an optical tweezers apparatus. As the temperature of the solution surrounding a captured molecule was increased from 11 degrees C to 52 degrees C in 500 mM NaCl, the overstretching transition force decreased from 69 pN to 50 pN. This reduction is attributed to a decrease in the stability of the DNA double helix with increasing temperature. These results quantitatively agree with a model that asserts that DNA melting occurs during the overstretching transition. With this model, the data may be analyzed to obtain the change in the melting entropy DeltaS of DNA with temperature. The observed nonlinear temperature dependence of DeltaS is a result of the positive change in heat capacity of DNA upon melting, which we determine from our stretching measurements to be DeltaC(p) = 60 +/- 10 cal/mol K bp, in agreement with calorimetric measurements.     

Bending, hydration and interstitial energies quantitatively account for the hexagonal-lamellar-hexagonal reentrant phase transition in dioleoylphosphatidylethanolamine.

We have accounted for the unusual structural change wherein dioleoylphosphatidylethanolamine undergoes a hexagonal-lamellar-hexagonal transition sequence as the water content is reduced systematically. We describe the role played by the energies of bending, hydration, voids in hexagonal interstices, and van der Waals interaction in this transition sequence. We have used the X-ray diffraction and osmotic stress experiments on the two phases to derive the structural parameters and all of the force constants defining the energetics of the hexagonal and lamellar phases. We have calculated the chemical potentials of lipid and water in both phases and derived the phase diagram of the lipid with no free, adjustable parameters. The calculated temperature/osmotic stress and temperature/composition diagrams quantitatively agree with experiment. The reentrant transition appears to be driven by a delicate balance between the hydration energy in the lamellar phase and bending energy in the hexagonal phase, whereas the energy of voids in hexagonal interstices defines its energy scale and temperature range. Van der Waals attraction between the bilayers in the lamellar phase does not appear to be important in this transition.     

Probing alamethicin channels with water-soluble polymers. Size-modulated osmotic action.

Contrary to expectations based on heightened solution viscosity, alamethicin channels appear to speed up in the presence of water soluble polyethylene glycols (PEGs) and dextrans. Specifically, added polymers reduce the probabilities of transition to higher-conductance states but do not change channel lifetimes. They thereby shorten the duration of current "bursts." These modified probabilities and kinetics reveal the action of polymer osmotic stress to suppress channel formation. The osmotic action of large, fully excluded polymers shows that some 3,000 A3 of water are taken up by the channel from the solution upon each transition to an adjacent higher-conductance state. The partial osmotic action of incompletely excluded polymers reveals the extent of exclusion for different-size polymers. The partial exclusion thus measured agrees remarkably well with estimates using data on reduction of single-channel conductance by current-impeding polymers. One can relate the degree of each polymer's exclusion to its size and to the radius of the channel pore.