bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interaction of metal ions with nucleic acids and related compounds. II. Studies on Au(III)‐nucleic acid system
Authors: Pillai C. K. S. , Nandi U. S. 
Published: December 2004

AbstractThe nature of interaction of Au(III) with nucleic acids was studied by using methods such as uv and ir spectrophotometry, viscometry, pH titrations, and melting‐temperature measurements. Au(III) is found to interact slowly with nucleic acids over a period of several hours. The uv spectra of native calf‐thymus DNA 9pH 5.6 acetate buffer containing (0.01MNaCIO4) showed a shift in λ max to high wavelengths and an increase in optical density at 260 nm. There was a fourfold decrease in viscosity (expressed as ηsp/c). The reaction was faster at pH 4.0 and also with denatured DNA (pH 5.6) and whole yeast RNA (pH 5.6). The order of preference of Au(III) (as deduced from the time of completion of reaction) for the nucleic acids in RNA > denatured DNA > DNA. The reaction was found to be completely reversible with respect KCN. Infrared spectra of DNA‐Au(III) complexes showed binding to both the phosphate and bases of DNA. The same conclusions were also arrived at by melting‐temperature studies of Au(III)‐DNA system. pH titrations showed liberation of two hydroxylions atr= 0.12 [r= moles of HAuCl4added per mole of DNA‐(P)] and one hydrogen ion atr= 0.5. The probable binding sites could be N(1)/N(7) of adenine, N(7) and/or C(6)O of guanine, N(3) of cytosine and N(3) of thymine.DNAs differing in their (G = C)‐contents [Clostridium perfingensDNA(G = C, 29%), salmon sperm DNA (G + C, 42%) andMicrococcus lysodeikticusDNA(G + C, 29%), salmon sperm DNA (G = C, 72%)] behaved differently toward Au(III). The hyperchromicity observed for DNAs differing in (G + C)‐content and cyanide reversal titrations indicate selectivity toward ( A + T)‐rich DNA at lw values ofr. Chemical analysis and job's continuous variation studies indicated the existence of possible complexes above and belowr= 1. The results indicate that Au(III) ions probably bind to hte phosphate group in the initial stages of the reaction, particularly at low values ofr, and participation of the base interaction also increases. Cross‐linking of the two strands by Au(III) may take place, but a complete collapse of the doulbe helix is not envisaged. It is probable that tilting of the bases or rotaiton of the bases around the glucosidic bond, resulting in a significant distrotion of the double helix, might take place due to binding of Au(III) to DNA.
Magnesium binding to yeast ribosomes
Authors: Walters J. A. L. I. , Van Os G. A. J. 
Published: December 2004

AbstractThis paper describes a theoretical and experimental analysis of the binding of magnesium ions to yeast, ribosomes. In the theoretical considerations the interactions between charges located on a macroion are included. In the calculations these interactions result in a term, in which both the charge and the radius of the macroion are accounted for. It appears that on dissociation of the ribosomes both the charge and the radius change, but in such a way, that the term, which accounts for the electrostatic interactions, remains constant. As a consequence the dissociation can lie neglected in the analyses of the binding experiments. Our experiments indicate that two binding reactions between ribosomes and magnesium ions occur. The endpoints of these reactions correspond to about 0.40 and 1.0 equivalent magnesium per ribosomal phosphate, respectively. The pK values are about 3.8 and 2.2, respectively. The experimental results indicate that the effect, of monovalent cations can be explained as a pure ionic strength effect, though the binding of monovalent cations could not be excluded completely.
Conformational dependence of the Raman scattering intensities from polynucleotides
Authors: Small Enoch W. , Peticolas Warner L. 
Published: December 2004

AbstractThe intensity of Raman scattering from the various Raman active vibrations of poly‐(riboadenylic acid), poly(ribocytidylic acid), poly(ribouridylic acid), and poly(riboinosinic acid) in moderately dilute solutions were examined as the temperature was changed to alter their conformation. It was found that certain highly intense, highly polarized Raman bands from the totally symmetric, i.e., in‐plane, ring vibrations of the nucleic acid bases become less intense as the chains become more ordered in solution. Since these vibrations occur at frequencies which are markedly different for each type of base, Raman spectroscopy appears to provide a new method for the characterizing of the average conformation of each of the bases in solution. A theory for the resonant Raman effect is given in which it is shown that, a decrease in resonant Raman intensity is to be expected if one obtains a decrease in the intensity of the corresponding ultraviolet absorption band with which the incident light is resonant. If it is assumed that certain Raman bands derive their intensity predominantly from the first few ultraviolet absorption intensities, then a qualitative explanation of our observed conformational dependence of the ordinary Raman intensities can be obtained.
Molecular orbital calculations on the conformation of polypeptides and proteins. II. Conformational energy maps and stereochemical rotational states of aromatic residues
Authors: Maigret Bernard , Pullman Bernard , Perahia David 
Published: December 2004

AbstractOur previous quantum‐mechanical calculations, by an all‐valence‐electrons method (PCILO) taking into account simultaneously the σ and π electrons of the system, on the conformation energy maps of the glycyl and alanyl residues are extended to the evaluation of these maps and of the stereochemical rotational states of the aromatic residues, phenylalanyl, tyrosyl, histidyl, and tryptophanyl in dipeptides. Calculations on model compounds are used for the predetermination of the side‐chain rotational angles χ1 and χ2 which are then used as selected parameters for the evaluation of the conformational energy maps as function of the backbone rotational angles Φ and ψ. The theory predicts that the most stable conformation for these aromatic residues should occur in the same region, around Φ = 200, ψ = 140°, in which it was predicted to occur for the glycyl and alanyl residues and which was completely overlooked by most of the previous “empirical” computations. Recent experimental work by a group of Russian authors using NMR and infrared techniques seems to confirm the theoretical result for the alanyl and phenylalanyl residues. The paper indicates also the secondary local minima which appear for the different residues. The theoretically allowed general conformational area for the four aromatic residues, within the reasonable value of 5 kcal/mole above the deepest minimum, is somewhat larger than the similar area allowed by the “hard sphere” empirical calculations. Practically all available representative experimental points from the study of small molecules and of the proteins lysozyme and myoglobin fall within the allowed area, the agreement being better with the results of the quantum mechanical calculations than with those of the “hard sphere” approximation. The values of the side‐chain rotational angles χ1 and χ2 and of their allowed combinations agree less satisfactorily with experiment, the experimentally observed combinations being more varied than the theoretically allowed ones. These last ones having, however, been predetermined on studies with model compounds, this situation is not astonishing. It is proposed to refine these results by a minimization with respect to the four parameters Φ, ψ, χ1, and χ2 involved.
Diffusion of DNA at very low concentrations
Authors: Strassburger J. , Rejnert K. E. 
Published: December 2004

AbstractThe diffusion behavior of DNA samples of molecular weights between 1 × 106 and 25 × 106 Daltons was investigated under standard conditions at mean concentrations c̄ between 0.0009 and 0.017 g/dl. Special techniques described previously were used and supplemented. The sensitivity required was accomplished by multiple passage through the sample cells (effective path length of 10–45 cm) and application of the Gouy interference method. The maximum DNA refraction index difference has been determined more precisely from Gouy interference fringes by applying a systematic variation procedure and a linear‐plot criterion. Convection was prevented by a temperature constancy better than 0.002°C/day, vibrationless operation, and by application of a slight density gradient of heavy water, which also improved the boundary‐forming procedure. The corresponding optical HDO gradient was compensated. The concentration dependence of the DNA diffusion coefficient average DA was found to be positive and very small at extremely low concentrations, that is, below c̄ = 0.008 g/dl, for the sample of highest molecular weight investigated. With beginning penetration of different DNA molecules, DA increases markedly. The diffusion constant averages of our polydisperse samples will be corrected for monodisperse subfractions in a following paper. The resulting molecular weights M from diffusion and sedimentation constants (D0, s0) together with data from literature are the basis of new s0–M, D0 − M, and [η]–M relations for monodisperse DNA samples.
DNA–copper(II) complex and the DNA conformation
Authors: Zimmer Ch. , Luck G. , Fritzsche H. , Triebel H. 
Published: December 2004

AbstractSpectrophotometric, sedimentation, infrared, optical rotatory dispersion (ORD), and circular dichroism (CD) methods have been used to demonstrate the structural changes in DNA induced by the interaction of copper(II) with bases and to elucidate the complex binding sites. As shown by the electrolyte‐induced reversion (addition of salts) of temperature‐denatured copper DNA the effectiveness of re‐formation of the double‐stranded structure depends on the temperature, copper(II) ion concentration, and on the base composition of the DNA. Exposure of heat‐denatured copper DNA to higher temperatures decreases the reversion effect on addition of electrolyte. The results indicate that a greater fraction with a cooperative transition appears on heating DNA to 80 or 100°C at a Cu2+/DNA‐P ratio of 2 : 1 than at a Cu2+/DNA‐P ratio of 1 : 1. With AT‐rich copper DNA, reversion to the native DNA structure was not observed. Selective methylation of guanine residues in DNA also affects the electrolyte‐induced reversion, indicating the importance of GC pairs for copper(II) binding and the reversion to the native structure. Temperature‐denatured copper DNA shows an increased sedimentation coefficient Which decreases again after electrolyte‐induced reversion. This change in s is reduced by selective methylation of DNA. Complex formation between copper(II) and the bases is accompanied by a conformational change of the DNA double‐helical structure as demonstrated by ORD and CD experiments. The ORD profile of GC‐rich DNA is much more affected by copper(II) than that of AT‐rich ones. Even at very low copper(II) concentrations, e.g., at 0.02 and 0.2 Cu2+/DNA‐P, the ORD and CD measurements exhibit conformational changes of the DNA secondary structure at room temperature. By comparing the infrared spectra of deoxynucleosides with that of DNA of different GC content it has been shown that both guanine and cytosine are involved in the formation of the complex of copper(II) with DNA. N‐7 and O at C‐6 in guanine and N‐3 as well as O of C‐2 in cytosine are discussed as the most probable binding sites in DNA. A binding model for the coordination of the copper(II) ion between guanine and cytosine of the opposite strands is suggested. The results are in good agreement with the assumptions and predictions made by Eichhorn and Clark about the complexing of copper(II) with DNA. The recent proposal made by Schreiber and Daune about an interaction of the type guanine–Cu2+–guanine cannot be excluded as an additional kind of coordination of copper(II) in DNA.
Fractionation of poly (dA‐dT) by gel chromatography
Authors: Jang Choong‐Gook , Bartl Paul 
Published: December 2004

AbstractA commercial sample of poly (dA‐dT), a copolymer of 2′‐deoxyribosyladenosine (dA) and 2′‐deoxyribosylthymidine (dT) of perfectly alternating sequence, was fractionated by chromatography on Agarose gel. Paucidisperse fractions of different molecular size were obtained. The plot of log s020,w values shows a linear dependence on Ve. The buoyant densities of individual fractions do not differ over the molecular size range studied. On the other hand, the heat‐induced hyperchromic effect was found to depend on molecular size below a certain limit, s020,w = 4.12 S.
Molecular orbital calculations on the conformation of polypeptides and proteins. V. Conformational energy maps and stereochemical rotational states of aliphatic residues
Authors: Maigret Bernard , Perahia David , Pullman Bernard 
Published: December 2004

AbstractThe quantum‐mechanical calculations by the PCILO method on the conformation of amino acid residues of proteins have been extended to the valyl, leucyl, and isoleucyl residues. In distinction to the earlier “empirical” computations, the quantum‐mechanical results indicate very similar energy contours for the stable conformations of the three residues. Their general outline is also similar to that of the alanyl residue, although reduced by about 25%. Contrary to the “empirical” computations, the present results predict that the region corresponding to the α‐helix should be one of great stability for the three residues and in particular for the valyl residue. The quantum‐mechanical results are in excellent agreement with the experimental conformations of the aliphatic residues in lysozyme and myoglobin. Their prediction as to the ready availability of the valyl residue in the α‐helical conformation agrees moreover with Ptitsyn's statistical evaluation of the participation of this residue in the inner turns of the helical regions in six globular proteins. The maximum conformational space allowed for the aliphatic residues is somewhat smaller than that allowed for the aromatic ones, while the minimum conformational space (region of stability common to all the residues) is similar in both groups.
Studies on the conformation of amino acids X. Conformations of norvalyl, leucyl and aromatic side groups in a dipeptide unit
Authors: Sasisekharan V. , Ponnuswamy P. K. 
Published: December 2004

AbstractBackbone‐side group conformations of amino acid residues including one or two δ‐carbons in the side group have been investigated. Conformational energies of norvalyl, leucyl, phenylalanyl, tyrosyl, tryptophenyl, and histidinyl side groups in a dipeptide unit have been calculated by using classical energy expressions. The side group conformations about the Cα—Cβ and Cβ—Cγ bonds are restricted to specific values of the respective rotational angles. Thus, most favourable positions of γ‐ and δ‐atoms of a linear side‐chain (norvalyl) are restricted to (γI, δII) (γII, δI), (γII, δII), (γIII, δII), and (γIII, δIII), whereas those of the side‐chain branching at a sp3 γ‐atom (leueyl) are further restricted. It is also shown that there is a definite correlation between the orientations of the two peptide planes and that of the planar group of the aromatic side chain of phenylalanyl type residues. The studies bring out an important fact that while the γ‐atoms have definite and characteristic effects on the backbone rotational angles ϕ and ψ, the δ atoms and beyond have no effects on the preferred ϕ and ψ values. Thus, the preferred backbone conformations are independent of the preferred side group conformations beyond the γ‐atom and vice versa. The observed ϕ, ψ, χ1, and χ2 values of amino acids, simple peptides, and of the three protein molecules lysozyme, myoglobin, and chymotrypsin have been compared with the theoretical predictions, and the agreement is found to be excellent.
Induced optical activity of acridine orange bound to poly‐S‐carboxymethyl‐L‐cysteine
Authors: Ikkda Shoiohi , Imae Toyoko 
Published: December 2004

AbstractThe absorption and rotatory properties of acridine orange‐poly‐S‐carboxymethyl‐L‐cysteine system in water and in 0.2 M NaCl have been measured at different pH and polymer‐to‐dye mixing ratios. The absorption spectra indicate that the dyes are bound to the polymer in dimeric or highly aggregated forms. At neutral pH where the polymer is randomly coiled, no optical activity is induced on the absorption bands of bound acridine orange. At acid pH where the polymer has the β‐conformation, a pair of positive and negative circular dichroic bands occur at each of the absorption bands, centered around 458 and 261 mμ. The signs of those bands are opposite to those found for α‐helical poly‐L‐glutamic acid. A model for the binding of dye to the β‐form polymer is presented, in which dimeric dyes are attached to ionized carboxyl groups and slack one another to form linear arrays on both sides of an extended polypeptide chain. The observed circular dichroism spectra can be explained by the Tinoco's exciton mechanism, based on this model. Low molecular weight poly‐S‐carboxymethyl‐L‐cysteine induces quite a different circular dichroism on bound acridine orange.
Thermodynamic analysis of thermal transitions in globular proteins. I. Calorimetric study of ribotrypsinogen, ribonuclease and myoglobin
Authors: Privalov P. L. , Khechinashvili N. N. , Atanasov B. P. 
Published: December 2004

AbstractThermal confonnalional transformations of globular proteins, chymotrypsinogen, ribo‐nudcase and myoglobin in solutions at different pH values were studied microcalorimetrically. It was shown that the heat effects observed in the process of heating have a complicated form and their explanation necessitates an assumption on the existence of two stages of the process separated by temperature: (I) a pre‐denaturational stage where the protein partial heat capacity changes are probably connected with a labilization of the globule structure and (II) a denaturational stage representing a single‐step transition of the protein into a state with a higher enthalpy. Transitions without enthalpy change, the existence of which is shown for the first time in globular proteins, necessitates a more cautions approach to the thennudynamical analysis of different physical parameters on the basis of the van't Hoff equation.
Configurational statistics of polysaccharide chains. Part III. Linear β‐(1 → 4′) xylan and mannan
Authors: Yathindra X. , Rao V. S. R. 
Published: December 2004

AbstractThe characteristic ratio CN = 〈r2〉0/Nlv2 of the β‐D(1 → 4′)‐linked polysaccharides xylan and mannan has been computed as a function of the angle τ at the bridge oxygen atom and the degree of polymerization N. The calculated values of the characteristic ratio CN are very high relative to their free rotational dimensions. The characteristic ratio of these polysaecharides converges to the asymptotic value at low degree of polymerization at higher τ values. The low values of the calculated characteristic ratio of xylan compared to cellulose and mannan for the same τ value indicate that the former is more flexible and assumes a compact configuration. A pronounced difference in the values of the characteristic ratio CN of cellulose and mannan has also been observed lower τ angles (<120°). On the other hand, nearly the same values of CN have been obtained at higher τ angles (120°–125°), which suggests that, cellulose and mannan may have similar configuralons in certain solvents.
Sensitized fluorescence in polynucleotide‐dye complexes and the problem of energy transfer in polynucleotides
Authors: Kaufmann M. , Weill G. 
Published: December 2004

AbstractNew results on sensitization of fluorescence of Profiuvine, Acridine Orange and Ethidium Bromide complexes wilh double stranded poly A‐poly U upon ultraviolet irradiation are presented. Together with older results on dye DNA complex, they are interpreted to show that base to base transfer plays essentially no role compared to direct base to dye transfer. A lower limit of base to base transfer time (which is at the same time a higher limit for life time of fluorescence) in DNA (2. 10−11 sec.) and poly A‐poly U (2. 10−13 sec.) is obtained which cast some doubt upon the validity of calculations of optical properties using the exciton (strong coupling) approximation.
Sedimentation velocity properties of catenated DNA molecules from HeLa cell mitochondria
Authors: Brown Irving H. , Vinograd Jerome 
Published: December 2004

AbstractCatenated molecules of closed circular DNA have been isolated from the mitochondrial DNA of HeLs cells. The sedimentation coefficients of several purified species have been investigated. The catenated dimer, made up of two interlocked duplex circles, sediments at 51 S in its superhelical (closed) form. Treatment with pancreatic DNase to relax the duplex circles converts the 51 S doubly closed dimer to a 42 S singly open species, then to a 36 S doubly open catenated dimer. The triply closed trimer sediments at 63 S and is converted to a 45 S triply open form by DNase. Electron microscopy of the DNA samples before and after DNase treatment shows that under the conditions used DNase does not change the catenated nature of the DNA. The measured sedimentation coefficients, have been compared with those estimated from previously proposed correlations of sedimentation coefficient and molecular weight, and with the sedimentation coefficients for catenated DNA presented by Wang. When all the interlocked circles in a catenane are relaxed, the DNA sediments about 5–10% faster than a relaxed multiple‐length circular molecule of the same molecular weight. The sedimentation coefficient, 36 S, of the fully relaxed catenated dimer is 1.4 times that of the relaxed monomer.
Polarization of fluorescence of an oriented solution of rodlike particles bearing a fluorescent label
Authors: Weill G. , Hornick C. 
Published: December 2004

AbstractThe variation of the polarized components of fluorescence of a rodlike particle bearing a fluorescent label upon partial orientation is calculated for some special geometry of the dye macromolecules complexes. Explicit expressions are given for the case where the energy of the molecule in the field depends only on one angle θ, showing that the result is a function of both 〈sin2θ〉 and 〈sin4θ〉. For the case of orientation in an electric field through an anisotropic induced moment, the expressions allow the calculation of this anisotropy of polarizability. The method is applied to the measurement of the polarizability of rodlike fragments of DNA labeled by intercalated molecules of Acridine Orange.
Concentration dependence in three‐component systems in sedimentation equilibrium in buoyant density gradients
Authors: Poon Pak H. , Schumaker Verne N. 
Published: December 2004

AbstractThe data on the band widths and band shapes of several DNA's at various concentrations in sedimentation equilibrium in a CsCl density gradient have recently become available. In the present report, these literature data are treated in the following manner: (1) based on a theory of isotope‐substitution, calculations are made of the molecular weights at infinite dilution, and (2) to explain the concentration dependence of band widths and band shapes, a theory of charge and hydration is put forth, and it is shown that by retaining the terms involving the charge of the macromolecules, it is possible to account for most of the concentration dependence.