Proton-NMR study of the interaction of trans-dichloro-diamine-platinum(II) with poly(I) and poly(I).poly(C)

The fixation of trans-(NH₃)₂Cl₂ Pt(II) to poly(I)·poly(C) at low r_b (< 0.05) leads to the formation of two complexed species. The major species (ca. 82% of bound platinum) involves coordination of platinum to a single hypoxanthine base, while the other species involves coordination of two hypoxanthine bases, which are either far apart on the same strand or on separate poly(I) strands, to the platinum. These same two species are found after reaction with poly(I), as are two other species throughout the entire r_b range studied (r_b = 0–0.30). The latter two species are assigned to trans-Pt bound to two bases on a poly(I) strand with (a) one or (b) two free bases between the two bound bases. These two species, (a) and (b), account for ca. 35% of the bound platinum, although the 1:1 species remains dominant (ca. 55%). These two additional species are observed at high r_b (>0.075) after reaction with poly(I)·poly(C) but as very minor species. They are formed by reaction with melted poly(I) loops. Also at high r_b, we have observed a shifted cytidine H⁵ resonance arising from interaction of trans-Pt with a melted loop of poly(C). Most probably, this arises from an intramolecular poly(I) to poly(C) crosslink. Results from the reaction of trans-Pt with poly(C) are presented for comparison.     

Interaction of poly(I) and poly(I)·poly(C) with chlorodiethylenetriamino platinum(II) chloride

The fixation of dien-Pt on poly(I)·poly(C) leads to only minor changes in the uv and CD spectra at ambient temperature, showing that there is little perturbation of the secondary structure in the r_b range studied (up to 0.30). However, the melting profiles show two steps. The T_m for strand separation increases linearly from 61°C (r_b = 0) to 80°C (r_b = 0.18), after which it declines on further increasing the r_b. The second melting step is not complete at 100°C, and the magnitude of the absorbance change in this second step also appears to be at a maximum at r_b = 0.18. Although dien-Pt can only coordinate to one base, the nmr spectra at 80°C also show a second type of interaction with the adjacent bases, which is only destroyed in the presence of a strong denaturing agent, 5M guanidinium hydrochloride. From these results and the spectrophotometric data, we observe that dien-Pt forms a triple sandwich by hydrogen bonding of the platinum amino groups to the adjacent hypoxanthine bases (N⁷). The presence of these hydrogen bonds accounts for the increased stability (maximal at one Pt to three hypoxanthine bases) and their rupture is seen in the second melting step. No interaction has been observed with poly(C) strand. Reaction of dien-Pt with poly(I) shows the formation of the same triple sandwich structure in the nmr spectra.     

Interaction of poly(I)·poly(C) with trans-dichloro-diammine-platinum (II)

The covalent binding of trans-Pt (NH₃)₂Cl₂ to the double-stranded poly(I)·poly(C) follows three types of reactions, depending on r_b and the concentration of polynucleotide in the reaction mixture. At r_b ? 0.1, the principal reaction is coordination to poly(I), giving rise to some destabilization of the double strand, as shown by uv and CD spectra, and a decrease in T_m values, giving rise to free loops of poly(C). At higher r_b and low polynucleotide concentration, the free cytidine bases react with platinum bound on the complementary strand to form intramolecular (interstrand) crosslinks that restabilize the double-stranded structure. At high r_b and high polynucleotide concentration, while the above reaction still occurs, the predominant one is the formation of intermolecular crosslinks. Under no conditions has strand separation been observed.     

Effect of non-complementary nucleotides on the rate of helix formation: kinetics of formation of poly (I)-poly (C,I) and poly (I)-poly (C,U) complexes

Apparent second-order rate constants for complex formation between poly (I) and poly (C) and copolymers of C containing non-complementary I or U residues have been determined spectrophotometrically. The rate constants decrease as the concentration of either I or U in the C strands increases–the effect seems insensitive to the species of residue involved, when differences in the thermal stabilities of the poly (I) poly (C,I) and poly (I). poly (C,U) complexes are taken into account. These results suggest that low concentrations of relatively stable defects can alter the apparent kinetic “complexity” of polynucleotides as determined by hybridization methods (C₀t analysis).     

Kinetic and equilibrium studies of the interactions of silver ions with poly(A)

The interaction of silver ions with poly(A) was studied by potentiometric titration, uv spectrophotometry, and stopped-flow spectroscopy. For 0 < r_b < 0.5, where r_b is moles of silver ion bound per mole of nucleotide base, there exists only one type of binding for poly(A). Using McGhee's theory, the binding parameters, such as intrinsic binding constant, number of sites per nucleotide, and cooperativity, were determined from the potentiometric titration data. Using the stopped-flow method, one relaxation time was observed in 0 < r₀ < 0.5, where r₀ is the moles of silver ions added per mole of nucleotide base. The concentration dependences of the relaxation time suggest that the binding of silver ions to poly(A) proceeds through the following mechanism: where M is free silver ions, P the free binding sites on poly(A), and C and C′ are two forms of the complex. The nature of the binding of silver ions to poly(A) is also discussed.     

Study of the interaction of cis-dichloro-(1,2 diethyl-3-aminopyrrolidine)Pt(II) complex with poly(I), poly(C) and poly(I) x poly(C)

The interaction of cis-dichloro-(1,2 diethyl-3-aminopyrrolidine)platinum(II) (Ptpyrr) with the polynucleotides poly(I), poly(C) and poly(I) x poly(C) acids was studied by circular dichroism, molecular fluorescence and (1)H NMR spectroscopies. Multivariate Curve Resolution, a factor analysis method, was applied for the analysis and interpretation of spectroscopic data obtained in mole ratio and kinetics studies. This procedure allows the determination of the number of different interaction complexes present during the experiments and the resolution of both concentration profiles and pure spectra for all of them. Two different interaction complexes were observed at the experimental conditions studied. The first one, at low Ptpyrr:polynucleotide ratio (r(Ptpyrr:poly)) values, corresponds to the interaction of Ptpyrr with hypoxanthine bases in the poly(I) moiety. This interaction leads to the destabilization and dissociation of the double-stranded conformation. The second complex was observed at higher r(Ptpyrr:poly) values and corresponds to the interaction of Ptpyrr to cytosine bases in poly(C) moiety. The formation of both complexes showed that the interaction of Ptpyrr with hypoxanthine bases occurred at the first stages of the reaction and with cytosine bases at longer reaction times. The results obtained show the utility of the Multivariate Curve Resolution approach for the analysis of data obtained by monitoring spectroscopically the interaction equilibria of platinum compounds with nucleic acids.     

Absorption and circular dichroism spectra of CuCl2 complexed with poly(S-carboxymethyl-L-cysteine) and poly(S-carboxyethyl-L-cysteine)

The interaction of CuCl₂ with poly(S-carboxymethyl-L -cysteine) (poly[Cys(CH₂COOH)]) and poly(S-carboxyethyl-L -cysteine) (poly[Cys(C₂H₄COOH)]) were studied by absorption spectra and circular dichroism (CD). On mixing CuCl₂ with polypeptide solutions, absorption bands appeared at 320–325 nm in both polypeptides, and at 255–260 nm in the case of poly[Cys(CH₂COOH)]. A stable bound species was formed in the case of poly[Cys(CH₂COOH)], since the apparent molar absorption coefficient of the bound species did not depend on the mixing ratio. From the absorption data, it was inferred that Cu²⁺ ions were complexed with the side chains, most probably with sulfur atoms and carboxyl groups. Induced optical activities were observed for the two polypeptides. The CD spectra of poly[Cys(CH₂COOH)] + CuCl₂ gave simpler aspects than those of poly[Cys(C₂H₄COOH)] + CuCl₂.     

Synthesis and crystal structure of tetrakis(dimethylsulfoxide) platinum(II) bis(triflouromethanesulfonate)

Crystals of Pt(DMSO)₄(TFMS)₂ have been prepared by dissolution of platinum(II) hydroxide in a solution of CF₃SO₃H in DMSO and subsequent evaporation. The structure was determined by use of a CAD-4 diffractometer with monochromatic Mo Kα radiation. The space group is P with Z = 2, a = 8.630(2), b = 9.557(3), c = 16.659(3) Å, α = 73.33(2), β = 77.38(2) and γ = 79.19(3)°. The refinement converged to R = 0.056. The coordination around platinum is distorted square-planar with two S- and two O-bonded DMSO ligands in a cis-arrangement. The four donor atoms and the platinum are coplanar within 0.03 Å. There is a severe steric crowding between the two S-bonded DMSO molecules, which gives rise to a distortion of the bond angles around the platinum. The crowding is minimized as much as possible by a staggered arrangement of oxygen atoms and methyl groups of adjacent ligands. Pt---S bond lengths 2.208(3) and 2.205(4) Å are significantly shorter that those in the corresponding palladium complex, in accordance with a much stronger bond in the case of platinum. Bond length comparisons also indicate that ground state transinfluence of S-bonded DMSO probably is about the same in platinum and palladium complexes.     

Experimental thermodynamics of the helix--random coil transition. 3. Determination of the transition enthalpies of the helical complexes poly(I+C) and poly I in solution

The enthalpies of the helix-coil transitions of the ordered polynucleotide systems of poly(inosinic acid)–poly(cytidylic acid) [poly(I + C)], (helical duplex), and of poly (inosinic acid) [poly(I + I + I)], (proposed secondary structure: a triple-stranded helical complex), were determined by using an adiabatic twin-vessel differential calorimeter. Measuring the temperature course of the heat capacity of the aqueous polymer solutions, the enthalpy values for the dissociation of the helical duplex poly (I + C) and the three-stranded helical complex poly(I + 1 + 1), respectively, were obtained by evaluating the additional heat capacity involved in the conformational change of the polynucleotide system in the transition range. The ΔH values of the helix-coil transition of poly (I + C) resulting from the analysis of the calorimetric measurements vary between the limits 6.5 ± 0.4 kcal/mole (I + C) and 8.4 ± 0.4 kcal/mole (I + C). depending on the variation of the cation concentration ranging from 0.063 mole cations kg H₂O to 1.003 mole cations/kg H₂O. The calorimetric investigation of an aqueous poly I solution (cation concentration 1.0 mole/kg H₂O) yielded the enthalpy value ΔH = 1.9 ± 0.4 kcal/mole (I), a result which has been interpreted qualitatively following current models of inter- and intramolecular forces of biologically significant macromolecules. Additional information on the transition behavior of poly(I+ C)Was obtained by ultraviolet and infrared absorption measurements.     

Interaction of sodium decyl sulfate with poly(L-ornithine) and poly(L-lysine) in aqueous solution

The binding isotherms of sodium decyl sulfate to poly(L -ornithine), poly(D ,L -ornithine), and poly(L -lysine) at neutral pH were determined potentiometrically. The nature of a highly cooperative binding in all three cases suggests a micelle-like clustering of the surfactant ions onto the polypeptide side groups. The hydrophobic interaction between the nonpolar groups overshadows the coulombic interaction between the charged groups. The titration curves can be interpreted well by the Zimm–Bragg theory. The average cluster size of bound surfactant ions is sufficiently large to promote the β-structure of (L -Lys)_n even at a very low binding ratio of surfactant to polypeptide residue, whereas the onset of the helical structure for (L -Orn)_n begins after about 7 surfactant ions are bound to two turns of the helix. The CD results are consistent with this explanation.     

Microcalorimetric Investigation of DNA,poly(dA)poly(dT) and poly[d(A-C)]poly[d(G-T)] Melting in the Presence of Water Soluble (Meso tetra (4 N oxyethylpyridyl) Porphyrin) and its Zn Complex

Abstract

Thermodynamic parameters of melting process (δH_m, T_m, δT_m) of calf thymus DNA, poly(dA)poly(dT) and poly(d(A-C))·poly(d(G-T)) were determined in the presence of various concentrations of TOEPyP(4) and its Zn complex. The investigated porphyrins caused serious stabilization of calf thymus DNA and poly poly(dA)poly(dT), but not poly(d(A-C))poly(d(G-T)). It was shown that TOEpyp(4) revealed GC specificity, it increased T_m of satellite fraction by 24°C, but ZnTOEpyp(4), on the contrary, predominately bound with AT-rich sites and increased DNA main stage T_m by 18°C, and T_m of poly(dA)poly(dT) increased by 40 °C, in comparison with the same polymers without porphyrin. ZnTOEpyp(4) binds with DNA and poly(dA)poly(dT) in two modes—strong and weak ones. In the range of r from 0.005 to 0.08 both modes were fulfilled, and in the range of r from 0.165 to 0.25 only one mode—strong binding—took place. The weak binding is characterized with shifting of T_m by some grades, and for the strong binding T_m shifts by ～ 30–40°C. Invariability of ΔH_m of DNA and poly(dA)poly(dT), and sharp increase of T_m in the range of r from 0.08 to 0.25 for thymus DNA and 0.01–0.2 for poly(dA)poly(dT) we interpret as entropic character of these complexes melting. It was suggested that this entropic character of melting is connected with forcing out of H₂O molecules from AT sites by ZnTOEpyp(4) and with formation of outside stacking at the sites of binding. Four-fold decrease of calf thymus DNA melting range width ΔT_m caused by increase of added ZnTO- Epyp(4) concentration is explained by rapprochement of AT and GC pairs thermal stability, and it is in agreement with a well-known dependence, according to which ΔT～T_GC-T_AT for DNA obtained from higher organisms (L. V. Berestetskaya, M. D. Frank-Kamenetskii, and Yu. S. Lazurkin. Biopolymers 13, 193–205 (1974)). Poly (d(A-C))poly(d(G-T)) in the presence of ZnTOEpyp(4) gives only one mode of weak binding. The conclusion is that binding of ZnTOEpyp(4) with DNA depends on its nucleotide sequence.     

Metal complexs of poly (α-amino acids): Cu(II) chelates of acetoacetylated poly(L-lysine), poly(L-ornithine), and poly(L-diaminobutyric acid)

The cupric complexes of poly(N^ε-acetoacetyl-L -lysine), [Lys(Acac)]_n′ poly(N^δ-acetoacetyl-L -ornithine), [Orn(Acac)]_n′ and poly(N^γ-acetoacetyl-L -diaminobutyric acid), [A₂bu-(Acac)]_n, as well as of the model compound n-hexyl acetoacetamide, have been investigated by means of absorption, potentiometric, equilibrium dialysis, and CD measurements. While in the complex of the model compound, one chelating group is bound to one cupric ion, in the polymeric complexes two β-ketoamide groups are bound to Cu(II) under the same experimental conditions. The binding constant of cupric ions to the three polymers and the formation constant of the Cu(II)-nhexylacetoacetamide complex have been evluated. Investigation on the chiroptical properties of the three polymeric complexes shows that the peptide backbone does not undergo conformational transitions, remaining α-helical when up to 20% of the side chains are bound to Cu(II). The optical activity of the β-ketoamide chromophores is substantially affected by complex formation and is discussed in terms of asymmetric induction from the chiral backbone.     

Infinite dilution viscoelastic properties of poly(gamma-benzyl-L-glutamate) in m-cresol.

The real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ-benzyl-L -glutamate) in m-cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights M_r are 6.4 × 10⁴–17 × 10⁴. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with M_r > 10⁵ is interpreted in terms of three mechanisms appearing from low to high frequencies: end-over-end rotation, flexural deformation, and side-chain motion. For a sample with M_r < 10⁵, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side-chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].     

Comparison of the helix–coil conformational changes of poly(deoxyadenylate-deoxytymidylate) and poly(deoxyadenylate-deoxythymidylate) induced by variations of hydrogen-ion concentration

Double-helical poly(dG-dC) and poly(dA-dT) are DNA analogs in which the interactions between the two strands of the helix are, respectively, either the stronger G/C type or the weaker A/T type along the entire length of macromolecules. Thus, these synthetic polynucleotides can be considered as representatives of the most stable and the least stable DNA. In the investigations presented here, potentiometric titrations and stopped-flow kinetic experiments were carried out in order to compare the pH-induced helix–coil conformations (10°C and 150mM [Na⁺]) the pH of the helix–coil transition (pH_m) is 12.81 for poly(dG-dC) and 11.76 for poly(dA-dT). The unwinding of double-helical poly(dG-dC) initiated by a sudden change in pH was found to be a simple exponential process with rate constants in the range of 200–600 sec^?1, depending on the final value of the pH jump. The intramolecular double-helix formation of poly(dG-dC) was studied by lowering the pH of the solutions from a value above pH_m to that below pH_m in dilute solutions (15.5 ug/ml [polymer]). Under these conditions, the observed rewinding reactions displayed a major and two exponential phases, all of which were independent of polymer concentration. From the comparison of the results of poly(dA-dT) and poly(dG-dT) would unwind faster than poly(dG-dC). However, if the pH jumps are such that they present the same perturbation of these polymers relative to their pH_m values, no significant differences exist between the rates of helix–coil conformation changes of poly(dA-dT) and poly(dG-dC).     

Far-infrared absorption of nucleotides and poly(I)·poly(C) RNA

We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ～25 to ～500 cm^?1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm^?1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm^?1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm^?1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.     

Chiral copper(I)—thiolate clusters in metallothionein and glutathione

Metallothionein (MT) is a ubiquitous mammalian protein comprising 61 or 62 nonaromatic amino acids of which 20 are cysteine residues. The high sulfhydryl content imparts to this protein a unique and remarkable ability to bind multiple metal ions in structurally significant metal–thiolate clusters. MT can bind seven divalent metal ions per protein molecule in two domains with exclusive tetrahedral metal coordination. The domain stoichiometries for the M₇S₂₀ structure are M₄(S_cys)₁₁ (α domain) and M₃(S_cys)₉ (β domain). Up to 12 Cu(I) ions can displace the 7 Zn²⁺ ions bound per molecule in Zn₇–MT. The incoming Cu(I) ions adopt a trigonal planar geometry with domain stoichiometries for the Cu₁₂S₂₀ structure of Cu₆(S_cys)₁₁ and Cu₆(S_cys)₉ for the α and β domains, respectively. The circular dichroism (CD) spectra recorded as Cu⁺ is added to Zn₇–MT to form Cu₁₂–MT directly report structural changes that take place in the metal binding region. The spectrum arises under charge transfer transitions between the cysteine S and the Cu(I); because the Cu(I)–thiolate cluster units are located within the chiral binding site, intensities in the CD spectrum are directly related to changes in the binding site. The CD technique clearly indicates stoichiometries of several Cu(I)–MT species. Model Cu(I)–thiolate complexes, using the tripeptide glutathione as the sulfhydryl source, were examined by CD spectroscopy to obtain transition energies and the Cu(I)–thiolate coordination geometries which correspond to these bands. Possible structures for the Cu(I)–thiolate clusters in the α and β domains of Cu₁₂–MT are proposed. © 1994 Wiley-Liss, Inc.     

Conformational change of poly( -lysine) induced by lipid vesicles of dilauroylphosphatidic acid

The effect of negatively charged dilauroylphosphatidic acid (DLPA) vesicles on the conformation of poly( -lysine) was investigated by circular dichroism measurements. DLPA vesicles induced a confomiational change Of poly( -lysine) from the random coil to β-structure in 5 mM Tes, pH 7.0. The fraction of induced β-structure (F_β) was determined via a procedure of curve fit the observed spectra to the reference spectra. F_β increased linearly with the molar ratio, r, of DLPA to lysine residues up to r 0.7, and reached a saturation value of 1 at r > 1. Within the range 0.7 r 1, precipitation occurred. The effect of dilution of the negative charge on vesicle membranes was examined by mixing DLPA with dilauroylphosphatidylcholine (DLPC). Although the β-structure Of poly -lysine) was also induced by mixed vesicles, the saturation value of F_β decreased with decreasing DLPA content in mixed vesicles. The variation in saturation value of F_β with the composition of mixed vesicles was interpreted in terms of the change in average distance between DLPA head groups in mixed vesicles.     

Fluorescence decay of ethidium bromide in the presence of the Z-conformation of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride

A time-resolved fluorescence study of ethidium bromide (EB) in the presence of poly(dG-dC) and of poly(dG-dC) modified by chlorodiethylenetriamine platinum(II) chloride is presented under solvent conditions in which these polymers adopt the Z-conformation (high ionic strength). It is shown that these polynucleotides can intercalate a very small quantity of EB. The binding parameters have been determined. The fluorescence lifetime of EB is slightly higher when bound to the Z-conformation (?25 ns) than when bound to the B-conformation (?23.7 ns). The nature of the salt has been checked. In the presence of 2.5M NaClO₄, no transition from the Z-conformation to another conformation is observed when EB is added. On the contrary, in the presence of 4.25M NaCl, EB induces a cooperative transition from the Z-conformation to a conformation characterized by a much higher affinity for EB intercalation. In the case of poly(dG-dC) this last conformation is identical to the one observed at low ionic strength (B-conformation), but in the case of the platinated polymer this conformation is slightly different, as judged by the smaller value of the fluorescence lifetime of the intercalated EB.     

Age and growth of stargazer (Uranoscopus scaber L., 1758) in the southeastern Black Sea

A sample of 346 Uranoscopus scaber (L., 1758) was collected from the southeastern Black Sea between January 2002 and May 2005 in order to provide information on age, growth, length–weight relationship, and stomach contents of this species. Total length and total weight of sampled fish ranged from 5.2 to 21.9 cm and from 2.0 to 182.5 g, respectively. The sex ratio (1 : 1.98) was biased toward females (P < 0.05). Isometric growth was determined in the population. Length–weight relationships for all individuals were described by the parameters: a = 0.0167, b = 3.00, with the r² = 0.99. The population was composed of five age‐classes (I–V years). The von Bertalanffy growth parameters (±SE) and confidence limit (CL, 95%) for the entire population were: L_∞ = 26.31 ± 0.838 cm (CL: 24.66–27.96), k = 0.339 ± 0.023 1/year (CL: 0.294–0.385), and t_o = 0.087 ± 0.0346 year (CL: 0.019–0.155) (r² = 0.96). Growth performance index (Φ) was 2.37. The diet was composed of Gobius sp. (2.2%),Trachurus trachurus (2.1%), Merlangius merlangus euxinus (4.3%) and unidentified fish species (17.4%); 39.1% were unidentified remains.