Histone-induced conformational changes in DNA as probed by quasi-elastic light scattering.

Quasi-elastic light scattering as measured by intensity fluctuation (self-beat) spectroscopy in the time domain can be profitably used to follow both the translational diffusion D and the dominant internal flexing mode τ_int of DNA and its complexes with various histones in aqueous salt solutions. Without histones, DNA is found to have D = 1.6 × 10^?8 cm²/sec and τ_int ? 5 × 10^?4 sec in 0.8 M NaCl, 2 M urea at 20°C. Total histone as well as fraction F2A induce supercoiling (D = 2.6 × 10^?8 cm²/sec, τ_int ? 2.8 × 10^?4 sec) whereas fraction F1 induces uncoiling (D = 1.0 × 10^?8 cm²/sec, τ_int ? 9.4 × 10^?4 sec). Upon increasing the salt concentration to 1.5 M the DNA–histone complex dissociates (D = 1.8 × 10^?8 cm²/sec). Upon decreasing the salt concentration to far below 0.8 M, the DNA–histone complex eventually precipitates as a chromatin gel.     

Thermodynamic parameters of helix-coil transition in polypeptide chains. I. Poly-(L-glutamic acid)

The helix-coil transitions for poly(L -glutamic acid) (PGA) in 0.2M NaCl and in its mixture with dioxane were studied by the methods of spectropolarimetry, viscometry, and potentiometric titration at different temperatures from 8 to 50°C. The enthalpy and entropy differences between the helical and coillike states of uncharged PGA molecules were determined from the curves of potentiometric titration. The temperature dependence of the cooperativity parameter σ was determined by two methods: from the sharpness of transition and from the dependence of the intrinsic viscosity on the helical content in the transition region. In 0.2MNaCl, σ= (2.5 ± 0.5) × 10^?3 and practically does not depend on temperature, i.e., the cooperativity of the helix-coil transition is connected mainly with the entropy decrease in initiating helical regions (ΔS_i ≈ ?12 is mole of helical regions). On the contrary, initiation of a helical region in the water-organic solvent mixture is accompanied by a considerable enthalpy increase.     

Frequency dependence of the proton magnetic relaxation in aqueous solutions iof haemoproteins

The longitudinal proton magnetic relaxation times T₁ were measured for ferri (met)-and carbonmonoxy-bovine haemoglobin and equine myoglobin in 0.1 M KH₂PO₄ aqueous solutions near pH 6 at 5°C and 35°C from 1.5- to 60-MHz Larmor frequencies. It is concluded that the correlation time τ_C for the dipole–dipole interaction of electron and nuclear spins is in fact the electron (ferric) spin relaxation time τ_S being close to 1.5 × 10^?10 sec for both metHb and metMb at 5°C. At 35°C the paramagnetic relaxation rates are not determined solely by the relaxation of protons exchanging from the haem pocket with bulk solvent. Hence, τC at 35°C cannot be calculated from the dispersion data obtained at this temperature. The relevance of this for the determination of interspin distances r is discussed.     

Dielectric relaxation of DNA in aqueous solutions.

Using a four-electrode cell and a new electronic system for direct detection of the frequency differences specturm of solution impedance, the complex dielectric constant of calf thymus DNA (M_r = 4 × 10⁶) in aqueous NaCl at 10°C is measured at frequencies ranging from 0.2 Hz to 30 kHz. The DNA concentrations are C_p = 0.01% and 0.05%, and the NaCl concentrations are varied from C_s = 10^?4 M to 10^?3 M. A single relaxation regions is found in this frequency range, the relaxation frequency being 10 Hz at C_p = 0.01% and C_s = 10^?3 M. At C_p = 0.05% it is evidenced that the DNA chains have appreciable intermolecular interactions. The dielectric relaxaton time τ_d at C_p = 0.01% agrees well with the rotational relaxation time estimated from the reduced visocisty on the assumption that the DNA is not representable as a rigid rod but a coiled chain. It is concluded that the dielectric relaxiatioinis ascribed to the rotation of the molecule. Observed values of dielectric increment and other experimental findings are reasonably explained by assuming that the dipole moment of DNA results from the slow counterion fluctuation which has a longer relaxation time than τ_d.     

Dielectric relaxation of DNA solutions. IV. Effects of salts and dyes

The effects of salts (NaCl, LiCl, Me₄NCl, AgNO₃, MgCl₂, CuCl₂ and MnCl₂) and dyes (acridine orange and methylene blue) on the low-frequency dielectric relaxation (0.1 Hz–30 kHz) of dilute aqueous solutions of DNA were investigated with varying salt or dye concentrations. Both the dielectric relaxation time τ_D and the rotational relaxation time τ estimated from the reduced viscosity decrease in quite parallel ways with increasing M/P (M/P being the normality ratio of cation to phosphate residue), reflecting the contraction of DNA molecule due to electrostatic shielding and cation binding. The agreement between τ_D and τ through the whole range of M/P supports our previous conclusion that the low-frequency relaxation of DNA arises from rotation of the molecule. The dielectric increment Δε also decreases with increasing M/P on account of both the contraction of DNA and the decrease in effective degree of dissociation of DNA. Δε as a function of M/P is interpreted in terms of a quasi-permanent dipole due to counterion fluctuation. These effects of cations are the strongest for divalent cations and rather weak for Na⁺, Li⁺, and Me₄N⁺. Effects of dye on τ_D and Δε are also well explained by the rotation of DNA molecule with a quasi-permanent dipole due to counterion fluctuation on the basis of intercalation of dye at D/P < 0.2 (D/P being the molarity ratio of dye to phosphate residue) and external binding at 0.2 < D/P < 1.0.     

Synthesis and conformation of poly(L-lysyl-L-alanyl-L-alanyl), a sequence-ordered water-soluble copolymer

The sequence-ordered copolymer poly-(Lys-Ala-Ala) was synthesized by polycondensation of the N-hydroxysuccinimide ester of ε,Z-Lys-Ala-Ala and deprotection of the polymerization product. A fraction of molecular weight 13,000 obtained by ion-exchange chromatography was investigated. The polymer is freely soluble in water at all _pH values, and is completely digested by trypsin and elastase. From CD and ORD data it was concluded that in water at 1°C the ionized form (at _pH 6.5) of the polymer is helical. On heating, helix-coil transition curves were obtained with a midpoint, T_m, depending on salt concentration. In salt-free water T_m = 12.3°C and in 0.2M NaCl T_m = 28.5°C. Adding MeOH, causes an increase in the helical content of the polymer (half helicity at 20% MeOH, without salt, at 29°C). Guanidine·HCl was shown to decrease the helicity. At 1°C half helicity. The nonionized polymer helix is more stable (T_m～90°C). At the high pH, at 60°C, when concentration of the polymer is higher than 1.9 × 10^-2M, a precipitate is formed which redissolves on cooling with the original helicity. This does not occur in the presence of 50% MeOH. By comparison with polylysine it was concluded that replacing two-thirds of the lysine residues in polylysine by alanine leads to a polymer forming a more stable α-helix, when fully ionized. This is essentially due to the diminished coulombic repulsion. Uncharged lysine residues are comparable to alanine residues in their helix-forming tendency since the sequential polymer as well as one-third ionized polylysine are helical to approximately the same extent at room temperature.     

One hundred-fold acceleration of DNA renaturation rates in solution

Solvents which accelerate DNA renaturation rates have been investigated. Addition of NaCl or LiCl to DNA in 2.4M Et₄NCl initially increases renaturation rates at 45°C and then leads to a loss of second-order behavior. The greatest accelerations are seen with LiCl and dilute DNA. Volume exclusion by dextran sulfate is the most effective method of accelerating DNA renaturation with concentrated DNA. Addition of dextran sulfate beyond 10–12% in 2.4M Et₄NCl fails to increase the acceleration beyond approximately 10-fold. Accelerations of 100-fold may be achieved with 35–40% dextran sulfate in 1M NaCl at 70°C. No other mixed solvent system was found to be more effective, although acceleration may be achieved in solvents containing formamide or other denaturants. The acceleration in 2M NaCl occurs without loss of the normal concentration and temperature dependence of DNA renaturation and is also independent of dextran sulfate concentration if sufficient dextran sulfate is used. Dextran sulfate may be selectively precipitated by use of 1M CsCl.     

d-CpCpGpG and d-GpGpCpC self-complementary duplexes: Nmr studies of the helix-coil transition

We have monitored the helix-coil transition of the self-complementary d-CpCpGpG and d-GpGpCpC sequences (20mM strand concentration) at the base pairs, sugar rings, and backbone phosphates by 360-MHz proton and 145.7-MHz phosphorus nmr spectroscopy in 0.1M phosphate solution between 5 and 95°C. The guanine 1-imino Watson-Crick hydrogen-bonded protons, characteristic of the duplex state, are observed below 10°C, with solvent exchange occurring by transient opening of the tetranucleotide duplexes. The cytosine 4-amino Watson-Crick hydrogen-bonded protons resonate 1.5 ppm downfield from the exposed protons at the same position in the tetranucleotide duplexes, with slow exchange indicative of restricted rotation about the C-N bond below 15°C. The guanine 2-amino exchangeable protons in the tetranucleotide sequence exhibit very broad resonances at low temperatures and narrow average resonances above 20°C, corresponding to intermediate and fast rotation about the C-N bond, respectively. Solvent exchange is slower at the amino protons compared to the imino protons since the latter broaden out above 10°C. The well-resolved nonexchangeable base proton chemical shifts exhibit helix-coil transition midpoints between 37 and 42°C. The transition midpoints and the temperature dependence of the chemical shifts at low temperatures were utilized to differentiate between resonances located at the terminal and internal base pairs while the H-5 and H-6 doublets of individual cytosines were related by spin decoupling studies. For each tetranucleotide duplex, the cytosine H-5 resonances exhibit the largest chemical shift change associated with the helix-coil transition, a result predicted from calculations based on nearest-neighbor atomic diamagnetic anisotropy and ring current contributions for a B-DNA duplex. There is reasonable agreement between experimental and calculated chemical shift changes for the helix-coil transition at the internal base pairs but the experimental shifts exceed the calculated values at the terminal base pairs due to end-to-end aggregation at low temperatures. Since the guanine H-8 resonances of the CpCpGpG and d-CpCpGpG sequences exhibit upfield shifts of 0.6–0.8 and <0.1 ppm, respectively, on duplex formation, these RNA and DNA tetranucleotides with the same sequence must adopt different base-pair overlap geometries. The large chemical shift changes associated with duplex formation at the sugar H-1′ triplets are not detected at the other sugar protons and emphasize the contribution of the attached base at the 1′ position. The coupling sum between the H-1′ and the H-2′ and H-2″ protons equals 15–17 Hz at all four sugar rings for the d-CpCpGpG and d-GpGpCpC duplexes (25°C), consistent with a C-3′ exo sugar ring pucker for the deoxytetranucleotides in solution. The temperature dependent phosphate chemical shifts monitor changes in the ω,ω′ angles about the O-P backbone bonds, in contrast to the base-pair proton chemical shifts, which monitor stacking interactions.     

On the hydration of DNA. I. Preferential hydration and stability of DNA in concentrated trifluoroacetate solution

The hydration of DNA is an important factor in the stability of its secondary structure. Methods for measuring the hydration of DNA in solution and the results of various techniques are compared and discussed critically. The buoyant density of native and denatured T-7 bacteriophage DNA in potassium trifluoroacetate (KTFA) solution has been measured as a function of temperature between 5 and 50°C. The buoyant density of native DNA increased linearly with temperature, with a dependence of (2.3 ± 0.5) × 10^?4 g/cc-°C. DNA which has been heat denatured and quenched at 0°C in the salt solution shows a similar dependence of buoyant density on temperature at temperatures far below the T_m, and above the T_m. However, there is an inflection region in the buoyant density versus T curve over a wide range of temperatures below the T_m. Optical density versus temperature studies showed that this is due to the. inhibition by KTFA of recovery of secondary structure on quenching. If the partial specific volume is assumed to be the same for native and denatured DNA, the loss of water of hydration on denaturation is calculated to be about 20% in KTFA at a water activity of 0.7 at 25°C. By treating the denaturation of DNA as a phase transition, an equation has immmi derived relating the destabilizing effect of trifluoroacetate to the loss of hydration on denaturation. The hydration of native DNA is abnormally high in the presence of this anion, and the loss of hydration on denaturation is greater than in CsCl. In addition, trifluoroacetate appears to decrease the ΔHof denaturation.     

Salinity and Temperature Effects on Germination for Three Salt-resistant Euhalophytes, Halostachys caspica, Kalidium foliatum and Halocnemum strobilaceum

The effects of three salinities (0, 100 and 500 mM NaCl) and four constant temperatures (10, 20, 30 and 35 °C) on seed germination of Halostachys caspica (M. B.) C. A. Mey., Kalidium foliatum (Pall.) Mop. and Halocnemum strobilaceum (Pall.) Bieb. were investigated. After seeds were treated with different concentrations of NaCl at constant temperatures of 10–35 °C for 16 days, ungerminated seeds were transferred to distilled water for 10 days to investigate the total germination; after this time, the ungerminated seeds from the 10 and 20 °C treatments were then moved to 35 °C for another 5 days to determine the final germination. The three plant species in the present experiment are salt-resistant euhalophytes growing in high saline soils in the Zhungur Basin in Xinjiang, a northwest province of China.Compared with germination under control conditions, germination percentages of all three species were not affected by 100 mM NaCl at 10–35 °C, while severely inhibited by 500 mM NaCl; germination percentages were very low at 10 °C up to 100 mM NaCl for all species; the optimum temperature for germination of H. caspica and K. foliatum was 20–30 °C, while 35 °C for H. strobilaceum, up to 100 mM NaCl; seeds did not suffer ion toxicity for all species, as evidenced by the high total germination after ungerminated seeds pretreated with 500 mM NaCl were transferred to distilled water at constant temperatures of 10–35 °C for 10 days, and the high final germination after the ungerminated seeds from the 10 and 20 °C treatments were subsequently moved to 35 °C for another 5 days; Halostachys caspica had greater sensitivity to increasing temperatures from 10 and 20 °C to 35 °C compared with the other two species.     

Rates of stomatal opening in conifer seedlings in relation to air temperature and daily carbon gain

Experiments were conducted on well watered 1-year-old Douglas fir [Pseudotsuga menziesii (Mirb.) Franco], western hemlock [Tsuga heterophylla (Raf.) Sarg.] and western redcedar (Thuja plicata Donn) seedlings to determine the effects of temperature on whole-plant photosynthetic and stomatal responses to short-term fluctuations in irradiance (Q). Following a step change in Q, time constants (τ, the period over which 63% of the total change occurs) for stomatal conductance (g_s) and assimilation rate (A) decreased linearly with increasing air temperature (T_air). For example, in western redcedar τ_A decreased from 30 ± 4 min at 5 °C to 10 ± 1 min at 25 °C. In all cases, τ_A was within 10–15% of τ_gs. There was considerable variation in τ among individuals within a given species. Differences between species became more pronounced with decreasing temperature. Multiplicative models that included functions for τ accounted for 99% of the diurnal variability in A and g_s for seedlings exposed to varying air temperature, irradiance and vapour pressure deficit. Estimates of daily A were within 2% of those measured. Intermittent cloud cover and understory shading were approximated by exposing seedlings to 3–4 episodes (≥1 h) of shade (200 or 500 μmol m^?2 s^?1) or complete darkness during the day. In such cases, daily A was overestimated by up to 4 and 21%, respectively, if a function for τ was excluded from the models. Our results suggest that there is scope for selecting seedling stock for increased carbon assimilation on the basis of reduced time constants. For example, in western redcedar, a 40% reduction in τ could lead to increases in daily carbon gains of almost 5% depending on the frequency and degree of shading. If these daily gains were translated into increased dry matter production and compounded, seasonal gains would be even larger.     

Interaction of nucleic acids. VI. Interaction of purine with nucleic acids

The interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly-nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de-naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic-costacking mechanism. Results from studies on optical rotation and helix-coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg⁺⁺ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20–40°C lower) in the presence of purine (0.2–0.6M).     

Thermodynamic parameters of helix-coil transition in polypeptide chains. II. Poly-L-lysine

The helix–coil transitions for poly-L -lysine (PL) were investigated by the methods of spectropolarimetry, viscometry and potentiometric titration in 0.2M NaCl at different temperatures as well as in 0.2MNaBr, 1MKCl, and in mixtures of 0.2MNaCl or NaBr with methanol at room temperature. The enthalpy and entropy differences between the helical and coillike states of uncharged PL molecules in 0.2.M NaCl were determined from the potentiometric titration curves. The cooperativity parameters σ for PL in different solvents were determined by two methods (from the sharpness of the transition and from the dependence of the intrinsic viscosity on the helical content in the transition region). In 0.2MNaCl σ has a value of (2.3 ± 0.5) × 10^?4 and does not depend on temperature, i.e., the cooperativity of the helix-coil transition, as for PGA, is mainly of an entropy origin (the initiating of the helical region is accompanied by the entropy decrease ΔS_i = ?12 eu/mole of helical regions). A comparison of the obtained results for PGA and PL with the molecular theories of the helix-coil transitions shows that the role of dipole-dipole interactions of nonneighboring peptide groups is greatly overestimated in these theories, leading to a considerable enthalpy contribution to the free energy of initiating helical regions which is not observed in the experiment.     

A critical evaluation of models for complex molecular dynamics: application of NMR studies of double- and single-stranded DNA

The nature of internal and overall motions in native (double-stranded) and denatured (single-stranded) DNA fragments 120–160 base pairs (bp) long is examined by molecular-dynamics modeling using ¹³C-nmr spin-relaxation data obtained over the frequency range of 37–125 MHz. The broad range of ¹³C frequencies is required to differentiate among various models. Relatively narrow linewidths, large nuclear Overhauser enhancements (NOEs), and short T₁ values all vary significantly with frequency and indicate the presence of rapid, restricted internal motions on the nanosecond time scale. For double-stranded DNA monomer fragments (147 bp, 24 Å diam at 32°C), the overall motion is that of an axially symmetric cylinder (τ_x = ～10^?6 s;τ_Z = ～1.8 × 10^?8s), which is in good agreement with values calculated from hydrodynamic theory (τ_x = ～1.8 × 10^?6 s; τ_Z = ～2.7 × 10^?8 s). The DNA internal motion can be modeled as restricted amplitude internal diffusion of individual C? H vectors of deoxyribose methine carbons C1′, C3′, and C4′, either with conic boundary conditions (τ_w = ～4 × 10^?9 s, θ_cone = ～21°) or as a bistable jump (τ_A = τ_B = ～2 × 10^?9 s, θ = ～15°). We discuss the critical role in molecular-dynamics modeling played by the angle (β) that individual C? H vectors make with the long axis of the DNA helix. Heat denaturation brings about increases in both the rate and amplitude of the internal motion (described by the wobble model with τ_W = ～0.2 × 10^?9 s, θ_cone = ～50°), and overall motion is affected by becoming essentially isotropic (τ_x = τ_Z = ～5 × 10^?8 s) for the single-stranded molecules. Since ¹³C-nmr data obtained at various DNA concentrations for C2′ of the deoxyribose ring is not described well by the above models, a new model incorporating an additional internal motion is proposed to take into account the rapid, extensive, and weakly coupled motion of C2′.     

Multinuclear magnetic resonance studies of collagen molecular structure and dynamics

We have measured the percentages of cis and trans Gly-Pro and X-Hyp peptide bonds in thermally unfolded type I collagen. ¹³C-nmr solution spectra show that 16% of the Gly-Pro and 8% of the X-Hyp bonds are cis in unfolded chick calvaria collagen. These results support the hypothesis that cis–trans isomerization is that rate-limiting step in the propagation of the collagen triple helix. We have used multinuclear solid-state nmr to study the molecular dynamics of the collagen backbone in tendon, demineralized bone, and intact bone as a function of temperature, hydration, and pH. These studies show that collagen backbone motions are characterized by a broad distribution of correlation times, τ, covering the range from 10^?4 to 10^?9 s. In the case of nonmineralized collagen, the root-mean-square fluctuations in azimuthal angle, γ_rms, range from ca. 10° when τ ～ 10^?9 s to ca. 30° when τ < 10^?4 s; in the case of bone collagen, γ_rms values are about half as large as those found in nonmineralized collagen. Backbone motions are negligible at temperatures below ?25°C. This is also the case at 22°C when demineralized bone collagen is lyophilized. In contrast, flexibility of hydrated demineralized bone collagen greatly increases as pH is lowered from 7 to 2. The more limited flexibility observed at neutral pH is a consequence of the intermolecular interactions that contribute to fibril organization and strength. However, the fibrils retain significant flexibility at physiological pH, enabling them to distribute stress and dissipate mechanical energy.     

The effects of aqueous neutral-salt solutions on the melting temperatures of deoxyribonucleic acids

The helical stability of a variety of DNA samples, ranging in base composition from 0 to 72 mole-% GC, has been studied by heat denaturation at neutral pH in increasing concentrations of LiCl, NaCl, KCl, CsCl, Li₂SO₄, and K₂SO₄. The variation of melting temperature with average base composition, dT_m/dX_GC, was found to decrease drastically in the concentrated salt media, e.g., from 41°C in 0.006M LiCl to 29°C in 3.2M LiCl, and from 39°C in 0.003M Li₂SO₄ to 18°C in 1.6M Li₂SO₄. At the same time, the thermal transition is much more cooperative in the concentrated salt solutions than at low ionic strength. Indeed, at limiting salt concentrations, the transition breadth seems to reach a minimum value irrespective of the compositional heterogeneity of the DNA samples. Attempts to correlate the observed decrease of dT_m/dX_GC with predicted changes in the enthalpy of melting, deduced from a simple theoretical treatment, experimental data on the binding of counterions and water to DNA, and experimental data on thermal denaturation, were unsuccessful. However, the strongly reduced composition dependence of the melting temperature can be understood in terms of a destabilizing effect of the concentrated salt media on GC-base pairs. It is suggested, though not proven, that the destabilization involves the displacement of water molecules from the DNA helix.     

Thermal denaturation of Na- and Li-DNA in salt-free solutions

Thermal denaturation of Na- and Li-DNA from chicken erythrocytes was studied by means of scanning microcalorimetry in salt-free solutions at DNA concentrations (C_p) from 4.5 · 10^?2 to 1 · 10^?3 moles of nucleotides/liter (M). Linear dependencies of DNA melting temperature (T_m) vs lgC_p were obtained: ((1)) ((2)) for Na- and Li-DNA, respectively. Microcalorimetry data were compared with the results of spectrophotometric studies at 260 nm of DNA thermal denaturation in Me-DNA + MeCl solutions at C_p ? (6–8) · 10^?5 M and C_s = 0–40 mM (Me is Na or Li, C_s is salt concentration). It was found that Eqs. (1) and (2) are valid in DNA salt-free solutions over the C_p range 6 · 10^?5?4.5 · 10^?2M. Protonation of DNA bases due to the absorption of CO₂ from air in Na-DNA + NaCl solutions affects DNA melting parameters at C_s < 4 mM. Linear dependence of T_m on lga₊ is found in Na-DNA + NaCl at C_s > 0.4 mMin the absence of contact of solutions with CO₂ from air (a₊ is cation activity). A dependence of [dT_m/dlga₊] on Li⁺ activity was observed in Li-DNA + LiCl solutions at C_s < 10 mM: [dT_m/dlga₊] increases from 17°–18° at C_s > 10 mM to 28°–30° at C_s ? 0.2–0.4 mM. Spectrophotometric measurements at 282 nm show that this effect was caused by protonation of bases in fragments of denatured DNA in neutral solutions. The Poisson–Boltzmann (PB) equation was solved for salt-free DNA at the melting point. The linear dependence of T_m vs lgC_p was interpreted in terms of Manning's condensation theory. PB and Manning's theories fit the experimental data if charge density parameter (ξ) of denatured DNA is in the range 1.8–2.1 (assuming for native DNA ξ = 4.2). Specificity of Li ions in interactions with DNA is discussed. © 1994 John Wiley & Sons, Inc.     

Ethidium bromide binding to native and denatured poly(dA)poly(dT)

Isotherms of the EtBr adsorption on native and denatured poly(dA)poly(dT) in the temperature interval 20–70°C were obtained. The EtBr binding constants and the number of binding sites were determined. The thermodynamic parameters of the EtBr intercalation complex upon changes of solution temperature 20–48°C were calculated: 1.0·10⁶ M⁻¹≤K≤1.4·10⁶ M⁻¹, free energy ΔG ^o=−8.7±0.3 kcal/mol, enthalpy ΔH ^o≅0, and entropy ΔS ^o=28±0.5 cal/(mol deg). UV melting has shown that the melting temperature (T _m) of EtBr-poly(dA)poly(dT) complexes (μ=0.022,4.16·10⁻⁵ M EtBr) increased by 17°C as compared with the ΔT _m of free homopolymer, whereas the half-width of the transition (T _m) is not changed. It was shown for the first time that EtBr forms complexes of two types on single-stranded regions of poly(dA)poly(dT) denatured at 70°C: strong (K ₁=1.7·10⁵ M⁻¹; ΔG ^o=−8.10±0.03 kcal/mol) and weak (K ₂=2.9·10³ M⁻¹; ΔG ^o=−6.0±0.3 kcal/mol).The ΔG ^o of the strong and weak complexes was independent of the solution ionic strength, 0.0022≤μ≤0.022. A model of EtBr binding with single-stranded regions of poly(dA)poly(dT) is discussed.     

Equilibrium studies on neutral red-DNA binding.

Spectrophotometric binding studies were undertaken on the interaction of neutral red with native and heat-denatured, sonicated, calf thymus DNA in a 0.2M ionic strength buffer containing Tris–sodium acetate–potassium chloride at 25°C. The pK_A of neutral red was found to be 6.81. At pH 5 the binding of protonated neutral red was complicated even at low concentration ratios of dye to DNA. In the pH range 7.5–8.5 the tight binding process could be studied and it was found that both protonated and free base species of neutral red significantly bind with DNA having association constants (in terms of polynucleotide phosphate) of 5.99 × 10³ M^?1 and 0.136 × 10³ M^?1, respectively, for native DNA and 7.48 × 10³ M^?1 and 0.938 × 10³ M^?1, respectively, for denatured DNA. The pK_A value of the neutral red–DNA complexes were 8.46 for native DNA and 7.72 for denatured DNA. These results are discussed in terms of possible binding mechanisms.