bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsic viscosities of cyclic and linear λ DNA
Authors: Douthart Richard J. , Bloomfield Victor A. 
Published: December 2004

AbstractThe ratio of the intrinsic viscosities of the linear and circular forms of λ DNA, [η]L/[η]c, has been measured as a function of ionic strength in the range [Na+] = 0.6. M–0.03MCorrections were made for the presence of uncyclizable linear contaminant in circular preparations. By combining data in the literature on the ionic strength dependence of linear DNA of various molecular weights with that obtained here, it was possible to determine the expansion parameter εL as a function of [Na+]. εL is defined by the relation 〈L2〉 = b2N1+εL, where 〈L1〉 is the mean‐square end‐to‐end distance of a chain of N segments of length b. The empirical relation εL = 0.05 − 0.11 log [Na+] for native NaDNA at 25°C is found. When εL = 0, [η]L/[η]c extrapolates to 1.6, in good agreement with the theoretical prediction of 1.55. As εL increases, [η]L/[η]c increases, in agreement with a theory of Bloomfield and Zimm.
On the hydration of DNA. II. Base composition dependence of the net hydration of DNA
Authors: Tunis Mary‐Jane B. , Hearst John E. 
Published: December 2004

AbstractThe dependence of the net hydration of DNA on its base composition has been measured by density gradient ultracentrifugation of three DNA's in a series of cesium and lithium salt solutions of different water activities. Extrapolation to zero water activity showed the dependence of the partial specific volume on base composition to be very small for CsDNA and aero for LiDNA. At least 99% of the dependence of buoyant density on base composition can be accounted for on the basis of a differential hydration, with a mole of adenine–thymine pairs binding about 2 moles more water than a mole of guanine–cytosine pairs in CsCl.
Chemically reacting systems of the type A + B ⇄ AB. II. Osmometry
Authors: Adams E. T. , Pekar A. H. , Soucek D. A. , Tang L. H. , Barlow Grant , Armstrong J. L. 
Published: December 2004

AbstractThe osmotic pressure equation for nonideal, associating systems of the type nA +mB ⇄ AnBm, has been derived, by using the assumption yAnBm/yAnyBm = 1. This treatment can also be applied to related associations such as nA + mB ⇄ AB + AB2 + A2B + …. From osmotic pressure experiments on the pure reactants it is possible to obtain the molecular weights (MA and MB) of the reactants and also the virial coefficients (BAA and BBB) of the reactants. The osmotic pressure of a nonreacting mixture of A and B can be calculated from these measurements. It can be used along with osmotic pressure measurements on equilibrium mixtures of A and B to obtain expressions containing the equilibrium constant (or constants) and the cross‐virial coefficients (BAB and BBA). Several procedures are described for the evaluation of the equilibrium constant (or constants) and the BAB or BBA terms. It appears that this procedure is a general one which is applicable to associations of the type nA + mB ⇄ AB + A2B + AB2 + …. By correcting for nonideal behavior, one should then be able to apply it to any method available for analyzing ideal associations of the types considered here. In addition it is possible, subject to certain restrictions, to analyze associations of the type 3A + B ⇄ A2 + AB.
Effects of magnesium and formaldehyde on the sedimentation behavior of rat liver ribosomes
Authors: Petermann Mary L. , Pavlovec Amalia 
Published: December 2004

AbstractWhen rat liver ribosomes were dissociated by removing their magnesium, the two subunits had s,w of 52.6 and 28.1 S, and appeared to be quite asymmetrical. In 4M urea they became even more elongated. On restoration of magnesium, both subunits assumed more compact forms, 57.6 and 31.7 S, but only 28% of them formed larger aggregates. After brief treatment with formaldehyde, the magnesium‐free subunits still elongated in urea, but to a lesser degree than the controls. When magnesium was restored they changed to 53.4 and 31.7 S forms, but did not, aggregate. The ribosomal subunits were also separated by reducing the bound magnesium to a low level, then adding 2.2M urea. After the urea had been dialyzed out, most of the large subunits were still in a compact form and when the magnesium concentration was increased, most of the subunits did not reassociate to whole ribosomes. Formaldehyde‐treated subunits, however, did not reassociate. Even in their most compact forms, 60.0 and 35.5 S, both subunits had high frictional ratios. The 60.0 and 31.7 S forms were assumed to be the shapes that are seen in electron micrographs of negatively stained ribosomes. Both subunits seemed to be highly hydrated. Since the large subunit appeared to contain twice as much water as the small one, it might be a structure with either a deep channel or a hollow center.
Determination of the base pairing content of ribonucleic acids by infrared spectroscopy
Authors: Thomas George J. 
Published: December 2004

AbstractA method is described for determining the fractions of adenine‐uracil and guanine‐cytosine base pairs of partly double‐helical ribonucleic acids in aqueous solution. The method is based upon the ability to distinguish between paired and unpaired bases by means of infrared spectroscopy of their deuterium oxide solutions in the 1500–1800 cm−1 frequency region of the infrared spectrum. An application of the method to yeast ribosomal RNA is described. At 30°C, ribosomal RNA is 64± 6% paired (35% GC, 29% AU). The method can be applied to determine the fractions of Watson‐Crick base pairs at a given temperature in any RNA containing the four common bases in known ratios.
NMR studies in solution of poly‐L‐proline
Authors: Conti Filippo , Piatelli Massimo , Viglino Paolo 
Published: December 2004

AbstractThe isomerization of poly‐L‐proline in different solvents has been studied by NMR spectroscopy. Different resonance signals for the CHα protons have been obtained for the two different helical conformations of thus compound, namely form I and form II.
Spatial configurations of polynucleotide chains. III. Polydeoxyribonucleotides
Authors: Olson Wilma K. , Flory Paul J. 
Published: December 2004

AbstractThe virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean‐square end‐to‐end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C2′ in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C3′–O3′ bond of the deoxyribose residue in the C2′‐endo conformation; accessible rotations are confined to the range between 0° and 30° relative to the trans conformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r2〉0/nl2 calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C3′‐endo conformation and ≈21 with all residues in the C2′‐endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C3′‐endo and C2′‐endo conformational isomers present in a ratio of ∼1 to 9.
Copper(II)—DNA denaturation. II. The model of DNA denaturation
Authors: Liebe Donald C. , Stuehr John E. 
Published: December 2004

AbstractIn a continuing study of the denaturation of DNA as brought abought about by Cu(II) ions, results are presented for the dependence of Tm and τ (the terminal relaxation time) on ionic strength, pH, reactant concentrations, and temperature. Maximum stability of the double helix, as reflected by the longest relaxation times and highest Tm values, was observed between pH 5.3 and 6.2. Outside this range both Tm and τ decreased sharply. A second, faster relaxation time was deduced from the kinetic cureves. The apparent activation energies of the rapid and slow (“terminal”) relaxations were found to be 12 and 55 kcal/mole, respectively. Several lines of evidence led to the conclusions that (1) the rate‐determining step in DNA denaturation, when occurring in the transition region, is determined by chemical events and (2) the interactions which are disrupted kinetically in the rate‐determining step are those which account for the major portion of the thermal (Tm) stability of helical DNA.
Graphical approach to non‐ideal cases of self‐associating protein systems
Authors: Chun P. W. , Kim S. J. , Williams J. D. , Cope W. T. , Tang L. H. , Adams E. T. 
Published: December 2004

AbstractOur previous paper described graphical procedures for evaluating the mode of association in ideal discrete and indefinite cases. This paper concerns the application of such procedures in cases where the non‐ideality term BM1 must be considered. Bovine liver L‐glutamate dehydrogenase and lysozyme are used as model systems. Several graphical procedures for dealing with cases of 1 − m, 1 − m − n, or indefinite association are developed. The procedure is based on the evaluation of the weight‐fraction monomer with‐out prior calculation of BM1, using graphical analysis to evaluate the non‐ideality term.
Far ultraviolet optical activity of saccharide derivatives. I. Xylan and cellulose acetates
Authors: Mukherjee S. , Marchessault R. H. , Sarko A. 
Published: December 2004

AbstractOptial rotatory dispersion (ORD) and Circular dichroism (CD) spectra of several β‐1,4 xylan and cellulose acetates and some of their oligomers were investigated. The CD spectra proved considerably superior in terms of information content and interpretability. Comparison of the xylan and cellulose acetate series which also included partially substited cellulose acetates showed that the sign of the CD of the C(6) acetyl was negative. Likewise, the combined contribution of C(1) and C(4) to their equatorially substituted acetyls was positive (with C(1) definitely Positive) and the combined contribution of C(2)eq and C(3)eq negative. The solution conformations of both polysaccharide acetates appeared to be random. The CD of White birch xylan acetate which is substituted on the average at every tenth residue with a 4‐O‐methyl glucuronic acid substituent, was sensitive to it. The xylan oligomer series also illustrated that CD may be used to determine the degree of polymerization of these oligomers up to about 20.
Optical rotatory dispersion and circular dichroism of benzoyl polysaccharides
Authors: Keilich G. , Bittiger H. 
Published: December 2004

AbstractMeasurements of optical rotatory dispersion (ORD) and circular dichroism (CD) were made in the range of 400–205 nm for polysaccharide tribenzoates such as 2,3,6‐tri‐O‐benzoyl amylose (I), 2,3,4‐tri‐O‐benzoyl dextran (II), tri‐O‐benzoyl pullulan (III), 2,3,6‐tri‐O‐benzoyl cellulose (IV), 2,3,6‐tri‐O‐benzoyl mannan (V), and polyglycan dibenzoates such as 2,3,‐di‐O‐benzoyl amylose (VI), cellulose (VII), and mannan (VIII). All compounds exhibit Cotton effects in the region of their UV absorption bands (206–285 nm).Comparison of the corresponding di‐ and tribenzoyl polysaccharides shows a qualitative agreement in number, position and sign of the CD bands but differences in ellipticity magnitude. The disubstituted derivatives exhibit smaller amplitudes than the trisubstituted ones. The contribution of the C(6) chromophore (linked by a CH2‐group to the asymmetric C(5) atom) was determined to be of the same sign as the combined contribution of the C(2) and C(3) substituents.The CD bonds of the individual polysaccharide derivatives, which differ in number, sign, and position, were discussed in terms of the steric position of the single chromophores and the steric arrangement and interaction caused by the configuration of the polysaccharides. The optical behavior of these polysaccharide derivatives was found to be not strongly influenced by a definite chain conformation in solution.
Vibrational spectrum of cyclic tetra‐L‐alanine
Authors: Gupta V. D. , Singh R. D. 
Published: December 2004

AbstractA normal coordinate analysis for cyclic tetra‐L‐alanine molecule is reported. A comparison of amide modes and other low‐frequency vibrations sensitive to conformational changes is made with those in poly‐L‐alanine. Intramolecular coupling coefficients are calculated using perturbation treatment.
Distortion of optical properties in cylinders by absorbance flattening
Authors: Day L. A. , Hoppensteadt F. 
Published: December 2004

AbstractAn analysis is made of the magnitude of distortions in the measured absorbance, circular dichroism, optical rotation, and other spectral properties of cylindrical structures based on Duysens' description of the absorbance flattening phenomenon. The model calculations are made for isotropic particles having the same refractive index as the solvent. Exact integral expressions for coefficients relating optical properties of chromophores in cylindrical particles with those of isolated chromophores in solution are obtained for cylinders of any radius and height which have either random or perpendicular orientation with respect to the incident radiation. The results of numerical evaluation of the integrals for specific cases are presented to demonstrate the dependence of flattening on cylinder height, radius, extinction coefficient, and orientation.
Hydration mobility in peptide structures
Authors: Chirgadze Yu. N. , Ovsepyan A. M. 
Published: December 2004

AbstractThe structural behavior of hydrochlorides of poly‐L‐lysine and tetraglycine depends on water vapor pressure. At low relative humidities, structural rearrangements are slow. Water molecules catalyze these structural rearrangements; thus, in tetraglycine 1 H2O molecule per 10 peptide residues. Some general aspects of the mechanism of the hydration mobility in peptide structures are discussed.
Naegeli amylodextrin and its relationship to starch granule structure. II. Role of water in crystallization of B‐starch
Authors: Kainuma Keiji , French Dexter 
Published: December 2004

AbstractAlthough native B‐type starch loses its sharp X‐ray pattern on strong drying, the wet Nägeli amylodextrin prepared from such starch gives a sharp B‐pattern, that is only slightly reduced in sharpness by complete drying. Nägeli amylodextrin dried admixed with a noncrystalline “filler” (e.g., starch sirup) gives an X‐ray pattern essentially identical to that of the wet amylodextrin, except that the 16‐Å (No. 1) ring is greatly reduced in sharpness and intensity. Failure of the B‐structure to collapse during drying indicates that water is not intercalated between turns of a helix or otherwise required to maintain the geometry and packing arrangement of the starch molecular chains. Rather, for native starch granules or amylose fibers, water relieves intercrystallite strains and consequent crystallite distortion induced by strong drying. For Nägeli amylodextrin, the small molecules of starch sirup can penetrate the interstices between crystallites and prevent strain build‐up during drying. For native starch granules, the interstitial regions are gel‐like in character and less permeable to starch sirup molecules. A model for B‐starch is proposed, that employs intertwined (double) helices.
Renaturation of DNA in the presence of ethidium bromide
Authors: Huttpm James R. , Wetmur James G. 
Published: December 2004

AbstractThe rate of renaturation of T2 DNA has been studied as a fuction of ethidium bound per nucleotide of denatured DNA. The Binding constants and number of binding sites for ethidium have been determined by spectral titration for denatured DNA at 55, 65, and 75°C and for native DNA at 65°C in 0.4M Na+. The rate of renaturation of T2 DNA was found to be independentof ethidium binding up to 0.03 moles per mole of nucleotide. Above 0.03 moles, the rate drops off precipitously approaching zero at 0.08 and 0.06 moles bound ethidium per nucleotide at 65°C respectively. A study was also made of the use of bound ethidium fluorescence as a probe for monitoring DNA renaturation reactions.
An extended Hückel molecular orbital approach to the study of the electronic structures and barriers to Syn–Anti interconversion in Syn purine nucleosides
Authors: Jordan Frank 
Published: December 2004

AbstractThe total energy and the electronic properties of some syn purine nucleosides have been determined as a function of the rotation angle around the C–N glycosidic linkage. Invariably, the crystallographic coordinates provide a state lying at or very near the minimum on the potential energy curve according to the extended Hückel parametrization here employed. The ribose moiety always carries a net positive charge whereas the base is always negatively charged. Changes in dipole moment magnitudes for the overall structure as well as in net atomic charges are noted upon rotation around the glycosidic linkage indicating that potential functions for polynucleotides may be in error if such changes are ignored.
Single‐ and double‐strand breaks in 5‐bromouracil‐substituted DNA of B. subtilis and phage PBSH after irradiation with long‐wave length UV and their correlation to intramolecular energy transfer
Authors: Mönkehaus Friedrich , Köhnlein Wolfgang 
Published: December 2004

Abstract5‐Bromouracil‐substituted DNA was isolated form B. Subtilis and phage PBSH. The three DNA fractions of Different densities (TT, TB, and BB) were irradiated with u.v. (313nm). The number of single‐strand and double‐strand breaks was determined. The breakage rates are given. It was found that in hybrid DNA (TB) double‐strand breaks occur depending linearly on dose. In BB–DNA the observed double‐Strand bresks can be divided into two fractions with a linear and quadratic dose dependence respectively. The results can be explained by assuming intramolecular energy transfer from the BU‐containing strand to its complementary strand.
A calorimetric study of a polymer–monomer complex formed by polyuridylic acid 3′,5′‐cyclic AMP
Authors: Franck F. , Ackermann Th. 
Published: December 2004

AbstractThe existence of a soluble complex formed by polyuridylic acid (poly (U)) and 3′,5′‐cyclic AMP (cAMP) is demonstrated by u.v. extinction vs. temperature curves, optical rotation, equilibrium dialysis, and reaction calorimetry. The complex hasthe stoichiometry of 2 poly (U)‐cAMP and its formation is accompanied by an enthalpy change of −13.0 kcal/mole of base triplet. The introuction of an empirical factor α in the equations given by Damle2 and Crothers2 leads to the evolution of a ΔH value of −13.4 keal/mole. The parameter α is considered as a correction factor for the concentration dependence of the binding process. There is no relation between α and the reduction of monomer activity due to self‐association of monomers. The study of the binding process at several temperatures showed that the cooperativity parameter, σ, is independent of temperature and its value of 6.5 × 10−3 is in good agreement with σ = 5 × 10−3 for the poly (U)·poly(A) system.3
Studies on cytochrome c. Part I. Synthesis of the protected hexadecapeptide (sequence 1–16) of Baker's Yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Borin Gianfranco , Marchiori Fernando , Scoffone Ernesto 
Published: December 2004

AbstractThe general strategy for the synthesis by conventional procedure of N‐ and C‐terminal fragments and of the entire sequence of baker's yeast iso‐1‐cytochrome c is discussed. The synthesis of the N‐benzyloxycarbonylhexadecapeptide tert‐butoxycarbonylhydrazide corresponding to the sequence 1–16 of the apoprotein is described in detail.
Hydrolysis of poly‐L‐lysine by pronase
Authors: Sass R. , Thiemann W. 
Published: December 2004

AbstractPronase E is able to hydrolyze poly‐L‐lysine in 100% yield into the monomer L‐lysine. The experiments show an intermediate production of tri‐L‐lysine and di‐L‐lysine that are clipped off from the polymeric peptide. During the hydrolytic process a number of characteristic amino acids are released from the enzyme that may indicate its activation. Amino acids as well as mono‐L‐lysine are decomposed by pronase E after a period of several days.
The influence of nearest‐neighboring amino acid residues on aspects of secondary structure of proteins. Attempts to locate α‐helices and β‐sheets
Authors: Kabat Elvin A. , Wu Taite 
Published: December 2004

AbstractThe influence of nearest‐neighbor pairs of amino acids (n − 1) and (n + 1) on the conformation of amino acid (n) in proteins has been studied. From experimental data on eleven proteins of known three dimensional structures, our definition of an α‐helical domain in the Φ,Ψ plot has been reexamined and found to be satisfactory. On the same principle, a regular β‐sheet domain has been delineated. We then revised our 20 × 20 table of frequencies of occurrences of various conformations tabulating three values: α‐helical, β‐sheet, and neither. These frequencies were then used to locate the helixbreaking positions in cytochrome b5, papain, thermolysin, and calcium‐binding protein. In conjuction with the helical wheel method, they were useful for predicting the locations of most α‐helical segments. Similarly the β‐sheet breaking positions in papain were located and most of the β‐sheets found by X‐ray diffraction were close to or between these positions. Data on β‐sheets are extremely sparse so that extensive tests were not possible. The application of this method to abnormal hemoglobins suggested possible distortions of helices and in several instances correlated with abnormal properties of the hemoglobins and association with disease. The variable region of human immunoglobin heavy chains was found to have a very low α‐helical content though β‐sheet structures might exist.
Conformational changes of polypeptides in intense electric fields
Authors: Bean C. P. , Bennett A. J. 
Published: December 2004

AbstractEmploying a simple “all or none” statistical theory, a calculation is given of the phase diagram in electric field–temperature space for the helix–coil transition of a polypeptide with nonpolar residues but charged end groups. The principal results are (i) the transition field extrapolated to absolute zero is on the order of millions of volts per centimeter, (ii) the normal transition temperature of large molecules is predicted to be significantly affected by fields as low as 30,000 V/cm, and (iii) for temperatures just above the helix‐coil transition temperature, the application of a field to a large molecule causes an initial transition to the helix state and with a further isothermal increase of field the coil state returns. The theory is extended to the case of the unfolding of a globular protein in an electric field. The fields are somewhat lower than those for the helix‐coil transition and are always single‐valued at a given temperature. Lastly the effect of including the presence of charged residues is shown to decrease the estimated critical fields but keep them of the same order of magnitude as those given for the case of nonpolar residues.
Anomalies in sedimentation. II. Testing the entanglement hypothesis
Authors: Schumaker Verne N. , Zimm Bruno H. 
Published: December 2004

AbstractZones of T2 DNA were sedimented through uniform solutions of T7 DNA to determine if the smaller DNA molecules would become entangled in the larger. No entanglement could be demonstrated even at high DNA concentrations. It is suggested that molecular entanglement is not responsible for the sudden loss of DNA from solution which occurs in high centrifugal fields. This communication also includes observations on the effects of rotor speed on the sedimentation behavior of DNA in high centrifugal fields, distortion of zone shape at high concentrations, and hydrodynamic interactions between DNA and MS2 bacteriophage particles.