bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of thymine dimers on DNA: DNA hybridization
Authors: Kahn Michael 
Published: December 2004

AbstractDNA from bacteriophage T7 was irradiated at long ultraviolet wavelengths in the presence of silver ions. Such treatment leads to selective production of thymine: thymine dimers in DNA. The DNA was melted and the renaturation rate was determined as a function of thymine dimer content and renaturation temperature. Under “normal” hybridization conditions little change in the renaturation rate was observed even when 30% of the thymine was dimerized. This result is consistent with the view that up to a 15% change in the primary sequence of DNA dose not appreciably change the renaturation rate.
Interactions between purine derivatives: Electronic spectral studies. II. Excition interactions in the dimer of 6‐methylpurine in aqueous solution
Authors: Kelly G. R. , Kurucsev T. 
Published: December 2004

AbstractFrom a study of the concentration dependence of the ultraviolet absorption spectra of aqueous solutions of 6‐methylpurine, the spectra of monomeric and dimeric species have been derived. The dichroic spectrum of 6‐methylpurine in stretched poly(vinyl alcohol) films has been determined. The absorption envelope of 6‐methylpurine up to 44,000 cm−1 appears to include a low‐intensity nitrogen (π*,n) transition at the low wavenumber tail and two additional electronic transitions of dominant intensities. Both the experimental dichroic ratios and theoretical calculations suggest that the letter two transitions are in‐plane (π*,π) types. Analysis of the dimer species spectrum in terms of exciton interactions between molecules in “sandwich” conformation has been carried out. The interaction between the moments of the lowest energy (π*,π) transitions of the molecule in the dimer seems to result in transfer rates of energy of the order of 1013 sec−1 between the two molecules.
A circular dichroism study of the primary structures of three crab satellite DNA's rich in A:T base pairs
Authors: Gray Donald M. , Skinner Dorothy M. 
Published: December 2004

AbstractWe have measured the circular dichroism spectra and have obtained melting curves for samples of purified satellite DNA's from three species of crab, Cancer borealis, Gecarcinus lateralis, and Callinectes sapidus. Although all three satellite DNA's have the same density in neutral CsCl, their circular dichroism spectra and melting and reassociation characteristics are different, as are other properties of these DNA's. The circular dichroism spectra are analyzed to give estimates of nearest‐neighbor frequencies. We estimate that about 90% of the Cancer borealis satellite DNA and over 80% of the Gecarcinus lateralis satellite DNA consist of d(AT)n:d(AT)n sequences, while the serially repeating unit of the Callinectes sapidus satellite DNA may not contain any extended d(AT)n:d(AT)n sequences. The results from the circular dichroism spectra for the Cancer borealis, Gecarcinus lateralis, and the Callinectes sapidus satellite DNA's are in agreement with base composition analyses, which give 2.4, 8, and 25% G+C, respectively, for these DNA's.
A proposed solution for the determination of the ionization constants of sets of ionizing groups in proteins
Authors: Marini Mario A. , Martin Charles J. , Berger Robert L. , Forlani Luciano 
Published: December 2004

AbstractA mixture of acids with known pK′ and in a known concentration was dissolved to simulate the ionic character of hemoglobin. The titration curves of the mixture were obtained in water and 3.6 M KCl at 20°C. These curves were subjected to analysis by a reiterative curve‐fitting procedure to determine if one could evaluate both the group ionization constants and the numbers of groups. This approach was successful in that the calculated parameters were within the experimental error encountered in obtaining these constants on each of the model compounds. However, analysis for the electrostatic interaction parameter w indicated that there was a possible effect on the ionization of formic acid, pyridine, imidazole, and the α‐amino group of glycylglycine in water and on imidazole and the α‐amino group of glycylglycine in 3.6 M KCl.
An electron microscopic method for studying nucleic acid–protein complexes. Visualization of RNA polymerase bound to the DNA of bacteriophages T7 and T3
Authors: Koller Th. , Sogo J. M. , Bujard H. 
Published: December 2004

AbstractDouble‐stranded DNA can be readily adsorbed on mica or directly on carbon coated grids from the surface of solutions containing ethidium bromide, actinomine, or propidium diiodide. The DNA molecules are unfolded, well separated, and show a length distribution similar to molecules prepared by protein monolayer techniques.Since the intercalating dyes tested do not lead to an increased apparent diameter of the nucleic acid the method is useful for the study of nucleic acid–protein complexes. As a model, the binding of E. coli RNA polymerase to phage T7 and T3 DNA was examined under different conditions. The enzyme can easily be identified and its position along the DNA molecule can be mapped.
Syntheses and conformational studies of poly(Nε‐methyl‐L‐lysine), poly(Nδ‐methyl‐L‐ornithine), poly(Nδ‐ethyl‐L‐ornithine), and their carbobenzoxy derivatives
Authors: Yamamoto Hiroyuki , Yang Jen Tsi 
Published: December 2004

AbstractThe helix–coil transitions of poly(Nε‐methyl, Nε‐carbobenzoxy‐L‐lysine), poly(Nδ‐methyl, Nδ‐carbobenzoxy‐L‐ornithine), and poly(Nδ‐ethyl, Nδ‐carbobenzoxy‐L‐ornithine) in chloroform–dichloroacetic acid and their corresponding decarbobenzoxylated polypeptides in alkaline solutions were followed by optical rotation measurements. The introduction of a methyl or an ethyl group to the side chains of the carbobenzoxy derivatives of poly(L‐lysine) and poly(L‐ornithine) appeared to weaken the helical conformation at 25°C. The thermodynamic quantities of the three water‐soluble polypeptides were calculated from the data on potentiometric titrations at several temperatures. For uncharged coil‐to‐helix transition, ΔH = −370 cal/mol and ΔS = −1.1 eu/mol for poly(Nε‐methyl‐L‐lysine), and ΔH = −540 cal/mol and ΔS = −1.6 eu/mol for poly(Nδ‐ethyl‐L‐ornithine) (all on molar residue basis). The absolute values of ΔH and ΔS dropped in the region of pH‐induced transition and eventually both quantities became positive. The initiation factor σ was about 2 × 10−3, which was essentially independent of temperature. For poly(Nδ‐methyl‐L‐ornithine) the coil‐to‐helix transition was not complete even when the polymer was uncharged at high pH.
Synthesis and characterization of poly(LysAla3)
Authors: Wender D. B. , Treiber L. R. , Bensusan H. B. , Walton A. G. 
Published: December 2004

AbstractThe synthesis and characterization of poly(LysAla3) are described. The polytetrapeptide is a model for short sequences found in proelastin, and is presumably involved in desmosine or isodesmosine cross‐link formation in the native protein. Poly(LysAla3) is found to possess a mixture of conformations in aqueous solution dependent on molecular weight and pH. Low‐molecular‐weight (ca. 3000) material appears to be a mixture of random and extended helix at neutral pH. However, as the molecular weight is increased an increasing amount of α‐helix is observed rising to >50% for mol wt = 21,000. The α‐helical chain segments are thermally stable, melting to a mixture of extended and random forms at Tm = 25°C. High pH (10.5) promotes further α‐helix formation but at pH >11.0 the polypeptide becomes insoluble. The inference is that short chain segments of the peptide in elastin are unlikely to be α‐helical in the equilibrium state but may fluctuate through such a conformation.
The structure of native cellulose
Authors: Gardner K. H. , Blackwell J. 
Published: December 2004

AbstractNative cellulose has been shown to consist of a crystalline array of parallel chains, based on the X‐ray diffraction data for specimens from the sea alga Valonia ventricosa. The unit cell is monoclinic with dimensions a = 16.34 Å, b = 15.72 Å, c = 10.38 Å (fiber axis), and β = 97.0°. The space group is P21 and the cell contains disaccharide segments of eight chains. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data using rigidbody least squares procedures. The results show a preference for a parallel chain structure with specific chain polarity with respect to the c axis. The refinement places the CH2OH side chains approximately 20′ from the so‐called tg conformation, with a result that an 02′H…06 intramolecular bond is formed. The structure also contains an 03H…05′ intramolecular bond and an 06H…03 intermolecular bond along the a axis. All these bonds lie in the 020 planes, and the structure is an array of hydrogen‐bonded sheets. A major consequence of this work is that regular chain folding can be ruled out and cellulose is seen as extended chain polymer single crystals.
Two proposed general configurations for bacterial cell wall peptidoglycans shown by space‐filling molecular models
Authors: Oldmixon E. H. , Glauser S. , Higgins M. L. 
Published: December 2004

AbstractBacterial cell wall peptidoglycans are built from unbranched β‐(1 → 4)‐linked glycan chains composed of alternately repeating units of N‐acetylglucosamine and N‐acetylmuramic acid residues, with peptide side chains attached to the muramic acid residues. The glycan chains are interconnected by peptide bonds formed between the peptide side chains. Through the use of three‐dimensional molecular models, two configurations of the glycan strands and the peptide side chains are described, which by their constancy of form reflect the fundamental constancies of the covalent structures. Each of these two models will accommodate any chemical modification that has been observed in bacteria without change in the configuration of the peptide backbone. Some alterations in the chemical structure, which have been sought in bacteria, but not found, would not be tolerated by the models. In these models, glycan strands are parallel, with their lengths and widths predominantly in the plane of the cell wall. The cross‐bridging portions of the peptide side chains are at right angles to the glycan strand, in a separate, parallel plane. A compact model is presented in which the peptide side chain is closely appressed to the glycan strand and is stabilized by three hydrogen bonds per disaccharide–peptide subunit. In a second model, the peptide side chain is raised away from the glycan strand in an entirely extended configuration. The compact and extended forms are interconvertible. The thickness of a sheet of peptidoglycan would be from 10.6 to 11.1 Å for the compact model, and 19.1 Å for the extended model.
Studies on deoxyribonucleoprotein structure. Sedimentation behaviour
Authors: Osipova T. N. , Vorob'ev V. I. , Sibileva M. A. , Frisman E. V. 
Published: December 2004

AbstractThe sedimentation behaviour of DNP samples from calf thymus partially depleted of protein was studied. Upon transition from DNP to DNA a twofold decrease of the sedimentation constant, S02 0,W was observed. The translational friction coefficient f of DNP calculated from S02 0,W does not change at deproteinization, whereas the intrinsic viscosity [η] increases notably. Such difference in the dependence of f and [η] on the protein content is interpreted in terms of the theories for semirigid coils. The application of different models of DNP structure for the description of the hydrodynamic behaviour of DNP is considered. A model of the semirigid coil formed by a DNP chain partly folded into the superhelix seems to be most preferable.
DNA conformation in N,N‐dimethyl formamide–H2O solutions
Authors: Bressan G. , Rampone R. , Bianchi E. , Ciferri A. 
Published: December 2004

AbstractOptical density, viscosity, and light scattering measurements for calf thymus DNA in water–N,N dimethyl formamide (DMF) solutions are presented. DMF content varied between 0 and 60% (v/v) and DNA molecular weight varied between 15 × 106 and 0.5 × 106. Complementary measurements of the solubility of adenine, thymine, guanine, and cytosine in H2O–DMF mixtures are presented. The denaturation temperature of DNA, manifested by about a 35% increase of optical density, is gradually depressed by increasing DMF content. However, a significant increase of OD occurs even before (and even after) the denaturation point, when DMF content is increased isothermally. The intrinsic viscosity also exhibits a large decrease when DMF content is increased both before and after the denaturation point. Light scattering data for high‐molecular‐weight DNA in the predenaturation range indicate a decrease of the mean‐square radius and a constant molecular weight on increasing DMF content. The results, interpreted in terms of the wormlike chain of Kratky and Porod, indicate a large decrease of the persistence length of DNA. For low‐molecular‐weight DNA, radius and molecular weight increase with DMF content, indicating intermolecular aggregation. The formation of compact structures of native DNA is discussed in terms of an increased solubility of uncharged bases, and a decreased solubility of phosphate and deoxyribose groups, when a less polar environment is provided by the addition of DMF.
The interpretation of oligonucleotide maps. A theoretical study of nucleic acid digests with special reference to repeated diverged sequences
Authors: Slack Jonathan M. W. 
Published: December 2004

AbstractOligonucleotide mixtures produced by the digestion of RNA by specific nucleases can be defined in terms of isostichs (sets of common chain length), compositional isomers, and sequence isomers. Equations are derived to express the distribution of radioactivity on the isostich length, the distribution of compositional isomers on the isostich length, and the distribution of compositional isomers on the proportion of total radioactivity (“intensity”). It is shown how the properties of a “fingerprint” may be calculated from first principles, and conversely how the complexity of a sequence may be estimated from its fingerprint.The equations are tested by means of computer simulations of RNA digestions and their range of applicability is determined.The three distributions are used to analyze the digests of repetitious sequences. It is shown how the parameters of a diverged sequence family can, in a favorable case, be deduced from its fingerprint.
Buoyant densities of natural and synthetic DNA's in CsCl and Cs2SO4 considered as sequence‐dependent properties
Authors: Gray Donald M. , Gray Carla W. , Ratliff Robert L. , Smith David A. 
Published: December 2004

AbstractThe buoyant densities of natural and synthetic DNA's can be accurately interrelated if second‐neighbor influences are taken into account. We derive the following expressions, based partly on the buoyant densities of six synthetic DNA's, for the buoyant densities ρ (g/cm3) of DNA's having random sequences. In CsCl,

and in Cs2SO4,

.
In these equations, HG is the mole fraction of G : C base pairs in the DNA and the buoyant densities are calculated relative to densities for E. coli DNA of 1.703 and 1.426 (g/cm3) in CsCl and Cs2SO4, respectively.
Molecular weight and shape of the phycocyanin hexamer
Authors: Kato Masanori , Lee Wylie I. , Eichinger B. E. , Schurr J. M. 
Published: December 2004

AbstractThe hexamer of phycocyanin from Phormidium luridum has been isolated and purified by ammonium sulfate fractionation and gel chromatography. The protein is characterized by the sedimentation constant S°20, w = 10.2S, the diffusion coefficient D20, w = 4.73 × 10−7 cm2/sec, and intrinsic viscosity [η] = 3.89 ml/g. The molecular weight of the aggregate is 209,000. The shape and dimensions of the hexamer are discussed in terms of a model consisting of subunits arranged with C6 symmetry. The monomers, assumed to be spherical, are found to have a radius of 22 Å, and the diameter across the hexamer is 132 Å. The latter figure agrees closely with dimensions observed in electron micrographs.
Conformational change of the triple‐helical structure. III. Stabilizing forces in the triple helix
Authors: Sutoh Kazuo , Noda Haruhiko 
Published: December 2004

AbstractThe analysis of thermal melting curves of (PPG)n (n = 10, 12, 14, and 15) and (PPG)n(APG)m (PPG)n (2n + m = 15; m = 1, 3, and 5) revealed that the enthalpy and entropy changes accompanying the transition from the random coil to the triple helix are −2500 cal and −6.3 e.u. per one mole of the tripeptide of the form of Pro‐Pro‐Gly, and −3100 cal and −11.2 e.u. per one mole of the tripeptide of the form of Ala‐Pro‐Gly.The thermal instability of the triple helix composed of Ala‐Pro‐Gly sequences, compared to the helix of Pro‐Pro‐Gly sequences, is due to the larger entropy change of Ala‐Pro‐Gly (−11.2 e.u.) compared to that of Pro‐Pro‐Gly (−6.3 e.u.), not from the difference in the enthalpy change.The difference in the enthalpy change between Pro‐Pro‐Gly and Ala‐Pro‐Gly arises from the hydrophobic bond between two pyrrolidine rings of proline residues formed in the triple helix. Since the enthalpy change for the formation of hydrophobic bonds is positive, it is also concluded that only one hydrogen bond is formed in a tripeptide unit, regardless of the amino acid sequence. The enthalpy change for the formation of this hydrogen bond is −3100 cal/mol, and that of the hydrophobic bond between two pyrrolidine rings is +600 cal/mol.
Effect of agents affecting water structure on the uptake of saccharides by agar and polyacrylamide gels
Authors: Sigler K. 
Published: December 2004

AbstractUptake of D‐xylose, D‐glucose, lactose, and dextran 10 was studied in 3% and 12.5% polyacrylamide gels in the presence of 2 M LiCl, 2 M NaCl, 2 M KCl, 2 M RbCl, 2 M CsCl, 2 M MgCl2, 2 M CaCl2, 1 M NaF, 1 M NaI, 0.5 M guanidine thiocyanate, 0.5 M guanidine sulphate, and 0.5 M N,N′‐diethylurea. With the exception of N,N′‐diethylurea and, in some cases, LiCl, which had an accelerating effect, the compounds retarded considerably the uptake of saccharides by agar gel but had only a slight effect in polyacrylamide. The nature of the gel is thus of primary importance in interactions of this type. According to the magnitude of their effect on saccharide uptake, the salts used were arranged into several series. An attempt was made to correlate the effects of individual salts with their hydration properties. The strongest effect was found to be exerted by KCl, RbCl, and CsCl, i.e., by chlorides of cations possessing negative hydration shells.
A method for measuring sedimentation and diffusion of macromolecules in capillary tubes by total intensity and quasi‐elastic light‐scattering techniques
Authors: Loewenstein M. A. , Birnboim Meyer H. 
Published: December 2004

AbstractLight scattered from a macromolecular solution in a capillary tube is used to determine both the sedimentation and translational diffusion coefficients. The capillary tube is spun in a preparative centrifuge, removed, and placed in a light‐scattering photometer equipped with a scanning mechanism. The intensity distribution of scattered light along the tube represents the concentration profile in the tube and provides the measure of boundary migration. The sedimentation coefficient is determined from this measure and the applied centrifugal field. The diffusion coefficient is obtained from a time‐autocorrelation analysis of fluctuations in intensity of light scattered from any fixed point of the profile. These coefficients were obtained for two monodisperse systems, R17 bacteriophage and 28s ribosomal rat liver RNA. The molecular weights obtained from ratios of these coefficients are in good agreement with literature values. In the sedimentation analysis, deviations from linearity between boundary displacement and applied field were found to be less than 1%. This precision confirms that the boundary is stable for the capillary geometry even in the absence of a preformed density gradient. The sedimentation coefficients of identical samples were also measured with the Spinco Model E analytical ultracentrifuge; results of the two methods agree to within 4%.As a consequence of the capillary tube geometry and light‐scattering detection, sedimentation coefficients can be obtained from sample volumes of less than 100 μl. This detection techniques is thus far demonstrated to be at least an order of magnitude more sensitive than Schlieren optics, thereby useful when uv absorption is not applicable. For diffusion measurements there are also several inherent advantages. The diffusion coefficient is obtained from the identical sample, and scanning provides the capability to measure D from various parts of the sedimentation profiles and thereby directly explore concentration dependence, homogeneity, and integrity of the sample. The capillary tube with a layer of silicone oil over the sample and centrifugation provides an effective method to cleanse the solution and trap all dust.
Fluorescence correlation spectroscopy and nonideal solutions
Authors: Phillies George D. J. 
Published: December 2004

AbstractThe information that may be obtained from a fluorescence correlation spectroscopic study of a nonideal solution is considered. If all of the macromolecules in a two‐component solution are fluorescently labeled, the mutual diffusion coefficient will be measured. If only a few of the macromolecules in a solution are fluorescently labeled, the tracer diffusion coefficient will be obtained. Two nonideal systems that probably may usefully be studied with fluorescence correlation spectroscopy are proposed. The application of fluorescence correlation spectroscopy to studies of lateral diffusion in biological membranes is discussed; the form of the contribution to the fluorescence correlation spectrum of bulk motion within a membrane is noted.
Optical property of bovine plasma albumin between 2 and 82 eV
Authors: Inagaki T. , Hamm R. N. , Arakawa E. T. , Birkhoff R. D. 
Published: December 2004

AbstractThe optical constants of bovine plasma albumin in the form of a dry solid film have been determined in the 2–82 eV region of photon energy. The extinction coefficient k was obtained by transmission measurements on thin films on a calcium fluoride substrate and on ultrathin films of polystyrene supported by mesh screen. The refractive index n was determined by a Kramers–Kronig analysis using the measured values of k. The complex dielectric function ε and the energy‐loss function −Im(1/ε) for charged particles were derived from the data of n and k. The result for k exhibit, in addition to the well‐known absorptions at 4.4, 5.5, and 6.4 eV, a small peak at 7.6 eV, a shoulder around 9.7 eV, and a strong peak at 14.0 eV. A prominent peak at 22.7 eV in the energy‐loss function exhibits a large degree of collective nature.
Effects of metal ions on the structure and spectra of the peptide group
Authors: Balasubramanian D. , Misra B. C. 
Published: December 2004

AbstractThe interaction between salts of Groups IA and IIA and model aliphatic amides has been studied. The interaction has been monitored by calorimetry and spectroscopy. Among the alkali cations, lithium ion interacts strongest, while in Group II calcium appears to interact somewhat stronger than magnesium. The metal cation binds to the amide oxygen atom and causes alteration in the amide group geometry. As a consequence, significant alterations are seen in the infrared, nuclear magnetic resonance, ultraviolet, and circular dichroism spectra of the ligand peptide. These findings are suggested to be of importance to the conformational studies of polypeptides and proteins.