bluuebunny/crossref_metadata_2025 huggingface dataset:
Electrophoresis of DNA. I. On a relationship between electrophoresis and donnan equilibrium experiments on DNA
Authors: Ross Philip D.
Published: December 2004

A calculation based upon Gorin's equation for the electrophoresis of a rigid cylinder is used to compare the available results of electrophoresis and membrane equilibrium experiments on DNA. The distribution of chloride ions across a membrane impermeable to DXA is considered. For a reasonable choice of parameters, agreement within about 2% is obtained between the values calculated from electrophoresis and the results of membrane equilibrium studies over a twenty‐fold range of NaCl concentration.
Effect of glucosylation on sedimentation velocity of DNA from T2 and T6 coliphages
Authors: Davison Peter F. , Freifelder David
Published: December 2004

In order to study the effect of glucose substitution on the sedimentation velocities of the T‐even phage DNA's, T2 and T2*, and T6 and T6* bacteriophages were grown with H3and P32 labeling. Zone sedimentation of the DNA's isolated from these phagea showed that the glucosylated DNA's from both T2 and T6 sediment faster than the nonglucosylated molecules. Nonglucosylated DNA from TG and T2 phages sedimented with the same velocity, suggesting that the molecules of these phages are of the same length.
Electrical and hydrodynamical properties of polypeptides in solution. I. Poly(L‐glutamic acid) in methanol‐water mixtures
Authors: Matsumoto Mitsuhiro , Watanabe Hiroshi , Yoshioka Koshiro
Published: December 2004

The electric birefringence of poly(L‐glutamic acid) (PLGA) in methanol–water mixtures has been measured by the use of the rectangular pulse technique at 25°C. The permanent dipole moment, the anisotropy of electrical polarizability, and the optical anisotropy factor of PLGA in solution were obtained from the dependence of the steady‐state birefringence on the electric field strength. Further, the mean length of PLGA in solution was calculated by a parameter method developed for analyzing the decay curve of electric birefringence. The permanent dipole moment per unit length obtained from these studies was 2.96, 2.48, 2.30, 2.66 D/Å in pure methanol, 10, 30, and 50 vol‐% water, respectively. The increase of water content caused the decrease of the mean length and broadened the length distribution of PLGA. These results are discussed in relation to the viscosity and the electrical conductivity of PLGA solutions.
Deoxyribonueleate solutions: Sedimentation in a density gradient, partial specific volumes, density and refractive index increments, and preferential interactions
Authors: Cohen Gerald , Eisenberg Henryk
Published: December 2004

Density increments (∂ρ/∂c2)°μ in solutions of NaDNA in NaCl and CsDNA in CsCl were determined over a wide range of salt concentrations; calf thymus DNA, fragmented by sonic irradiation to a molecular weight of 4–6 × 105 was used. The partial specific volume v̄2° of NaDNA at 25°C was found to ho 0.500 ml/g in water, and that of CsDNA 0.440 ml/g. Both values increase with increasing NaCl and CsCl concentration. Refractive index increments under various experimental conditions were also determined. The relevance of the density increments (at constant, chemical potential of diffusible solutes) to equilibrium sedimentation in a density gradient and the evaluation of molecular weights is discussed. Distribution coefficients of diffusible components, sometimes referred to as preferential solvation or net hydration, were derived from the density increments and partial volumes and compared with direct experimental results, whenever available, from membrane distribution and isopiestic distillation. The thermo‐dynamic significance of the distribution coefficients as well as possible interpretations in terms of specific molecular mechanisms are considered.
Mechanochemical melting of collagen fibers. I. Mechanical contractions
Authors: Yonath J. , Oplatka A.
Published: December 2004

The correlation between mechanical and chemical Processes in the contractile system collagen fibers–aqueous KCNS sulutions was investigated. Melting and contraction of the fibers were induced by applying a force sufficiently high as to prevent melting in a KCNS solution and then decreasing it either suddenly, or continuously at a constant rate. The kinetics of both processes are characterized by an initial rapid elastic response of the crystalline collagen, followed by a stationary region. The force–velocity relationship in this region was found to be the same under different types of mechanical deformations. It is probable that under the prevailing conditions, the behavior in the stationary state is determined by the melting process and is not markedly influenced by diffusional changes. Part of the experimental data could be explained by assuming a linear, rigid model or, better, by taking into account the highly elastic properties of the amorphous collagen. The kinetic, unit seems to be composed of several hundred amino acid residues.
Mechanochemical melting of collagen fibers. II. Diffusion‐controlled contractions
Authors: Oplatka A. , Yonath J.
Published: December 2004

Collagen fibers were contracted “chemically,” i.e., by transferring them from water into KCNS solutions either isometrically or isotonically. Both changes in force and fiber length and in salt and water contents were measured as functions of time. The mechanical changes were found to follow the diffusional processes. The diffusion of water exhibited a plasmolytie effect. The role of water in the melting process is discussed.
Specific heat studies of various wool–water systems
Authors: Haly A. R. , Snaith J. W.
Published: December 2004

Measurements of specific heat of wool‐water systems were made at approximately 5°C intervals over the temperature range −70 to 100°C. Ten different, samples were used, each with a different amount of absorbed water in the range from dry ness to saturation at 0°C. The graph of specific heat against temperature for dry wool is precisely linear over the complete temperature range, suggesting that thermal motion is entirely vibrational. When absorbed water is present the data can be conveniently discussed in terms of behavior below and above an amount of absorbed water of 22.7 g in 100 g of wool (22.7% of absorbed water). Below 22.7% there is only one temperature range in which the results indicate an appreciable transition in heat absorbing properties. The temperature of transition depends on water content but is higher than 0°C. Above 22.7% a second transition appears in the range −30 to 0°C and grows rapidly larger with increase of water content. The first transition is tentatively ascribed to a slightly cooperative breakdown of polar bonds in wool, and the second to a process analogous to melting in the absorbed water. The results are discussed in these terms as well as with reference to specific heat theories, the heat absorption of the wool component and the water component, and enthalpy differences between the various samples.
Preparative fractionation of lignin by gel‐permeation chromatography
Authors: Kirk T. K. , Brown W. , Cowling E. B.
Published: December 2004

The combination of an agarose gel (Bio‐Gel A) and a dioxane–water (1:1) solvent system allowed the fractionation, on a preparative scale, of a very polydisperse, non‐derivatized lignin preparation (enzymatically liberated lignin prepared from sweetgum sapwood with Lenzites trabea). Three fractions differing markedly in molecular weight were obtained. A gel of crosslinked alkylated dextran (Sephadex LH‐20) with the same solvent system allowed division of the lowest molecular weight fraction into two fractions. These materials were characterized by measurements of intrinsic viscosity and number‐average molecular weights in dimethylformamide and dioxane–water. It was established that the two highest molecular weight fractions were associated in an average trimeric form in dioxane‐water (1:1) as compared to the form (considered to be molecular) that occurred in dimethylformamide. Molecular size distributions and eluant volumes of the fractions were determined with a Sephadex G‐100–formamide system, the latter being one of the most powerful nonaqueous solvents for lignin. Adsorption effects were known to be absent in this case, and the lignin molecules were considered to be unassociated in formamide. The four fractions were distinguishable with the formamide–G‐100 system, thus indicating that the original fractionation was based on molecular size. The enzymatically liberated lignin contained molecules that comprised a continuum of molecular weights from approximately monomeric to molecules that were at the limit of the solvating power of dioxane–water (1:1) and dimethylformamide. Limited physicochemical data were consistent with a compact, approximately spherically symmetric shape of the lignin in solution.
Experimental thermodynamics of the helix–random coil transition. II. Calorimetric measurement of transition enthalpies of poly A in acid aqueous solution
Authors: Klump H. , Ackermann Th. , Neumann E.
Published: December 2004

The enthalpy change accompanying the double helix–coil transition of polyriboadenylic acid (poly A) in aqueous solution has been measured optically and calorimetrically in the pH range 5.7–4.5. The course of this cooperative transition was followed optically by measuring changes in ultraviolet absorption as a function of temperature at different pH values, and calorimetrically by determining the heat capacity of the solution through the transition region. From the latter measurements, the enthalpy of transition was calculated. It is shown, that ΔH is dependent on pH as it is expected from the influence of protonation of the double helix of poly A.
Potentiometric titration of polyelectrolytes having stiff backbones
Authors: Muroga Yoshio , Suzuki Kazutoshi , Kawaguchi Yoshikazu , Nagasawa Mitsuru
Published: December 2004

The potentiometric titration curves of carboxymethylcellulose, which has a relatively stiff backbone, and also of poly(D‐glutamic acid) in the helical region are compared with the theoretical curves calculated assuming that the polyions are rods and have smeared charges on their surfaces. For carboxymethylcellulose good agreement is observed when its charge density is high, whereas as the charge density decreases the calculated curves deviate from the observed ones. The main reason for the disagreement at low charge densities may be attributed to the flexibility of the polymer backbone. For helical poly(D‐glutamic acid) satisfactory agreement between calculated and observed curves is found if a radius thicker than the realistic radius is employed. The reason for the excessively large radius may be attributed to the inapplicability of the smeared charge model.
The nucleic acid distribution function: Evaluation of the loop closure probability
Authors: De Lisi Charles
Published: December 2004

We present a detailed theoretical study of nucleic acid distance distribution functions for chain lengths up to thirty‐five nucleotides. The distribution functions were found by the Monte Carlo techniques described previously and, where they are symmetric, by reconstruction from their even moments. A comparison of the two approaches allows an assessment of the utility of expansion procedures for stiff chains (C∞ ≈ 17), as a function of length and extension. It was found that for chains with fewer than fourteen nucleotides over seventy even moments were required to obtain a reliable function for extensions R ≥ (〈R2〉)1/2. On the other hand at thirty‐five nucleotides the first ten even moments were sufficient to reconstruct the distribution for all but extreme extensions.

The other feature of the calculation is the prediction of a loop weighting function. It was found that for a thirty‐five nucleotide chain, the form of the distribution function is very nearly gaussian for R < (〈R2〉)1/2. Consequently a loop weighting function based on detailed crystallographic data is now known for all values of N. The first derivative of the function is within 8% of the Jacobson‐Stockmayer value at 170 nucleotides, but differs severely from the latter for chains with less than twenty nucleotides.
Effects of deuterium on the thermal stability of the poly A–poly U helix.
Authors: Klump H.
Published: December 2004

The effect of deuterium on the thermal stability of the polynecleotide double helix formed by the homopolymers polyadenylie acid (poly A)and polyuridylic acid (poly U)has been invertigated by measuring the best capacity as a function of temperature in an automatic scanning adiabatic calorimeter. Hydrogen‐bounded and deuterium‐bonded helical conformations of the polynecleotides used have been melted in H2O and D2O2 respectively, as solvent. Within the limits of experimental error, there is no dfference in the measured enthallpy change accompanying the helix‐random coil transition. The enthalpy change ΔH is 6.6 Kcal/MBP ub any case. The half‐conversion temperatures Tm differ by two degrees. Tm for poly (AU) in H2O is 45.8°C, Tm for poly (AU) in D2is 47.7.°C.
Volume effects in aqueous solutions of macromolecules containing non‐polar groups
Authors: Bøje Lars , Hvidt Aase
Published: December 2004

Specific volumes at 25° of aqueous solutions of poly(N‐methyl acrylamide) and poly‐(ethylene oxide) have been measured, and the data obtained is compared with corresponding data on low‐molecular‐weight compounds. The results support the notion, that the volume changes following the interaction between aliphatic groups and water are positive. They are discussed with particular reference to pressure effects on protein conformations.
Electrical properties of hydrated collagen. I. Dielectric properties
Authors: Tomaselli V. P. , Shamos M. H.
Published: December 2004

The effect of water on the low‐frequency (102‐105 Hz) complex permittivitv of native, sold‐state collagen has been investigated experimentally. Measurements at ambient temperature show that dry collagen exhibits essentially no frequency or temperature dependence. As water is absorbed, both dielectric constant and loss factor increase simultaneously and rise sharply upward at a hydration level which may be associated with the completion of the primary absorption layer as determined from independent water absorption studies. The behaviour is qualitatively identical to that observed for other proteins and related materials.

Temperature‐dependent measurements made under vacuum conditions in the range −196°C to +100°C are characteristic of the dielectric properties of the water in the sample. Dehydration produced by successive temperature recycling to the maximum temperature effectively eliminates any temperature or frequency dependence. A maximum in the temperature‐dependent curves is found at about +40°C and is explained as the superposition of two processes: (1) the transition of water molecules from bound to free states, and (2) the difffusion of water molecules out of the system.

The dielectric constant of dry collagen, after desorption at ambient temperature, is about 4.5. Desorption at elevated temperatures reduced the room temperature value to about 2.3 and the liquid nitrogen temperature value to a number indistinguishable from the optical value of n2 = 2.16.
A dihedral angle‐vicinal proton coupling constant correlation for the α–β bond of amino acid residues
Authors: Kopple Kenneth D. , Wiley Gary R. , Tauke Ralph
Published: December 2004

A coupling constant‐dihedral angle correlation for the HCαCβH system of amino acid residues in peptides has been derived from a set of model compounds covering the full range of dihedral angles. The expression obtained, J = 11.0 cos2 θ −1.4 cos θ + 1.6 sin2θ, is close to those already used in pmr studies of peptide conformation, and provides a firmer foundation for them. A factor limiting the precision of this and other “Karplus relations” is illustrated.
Anomalies in sedimentation. I. Stability theory of sedimenting entanglements in the “tight‐bending” limit
Authors: Goldstein Byron , Zimm Bruno H.
Published: December 2004

A simple model is introduced to investigate the stability of a sedimenting entanglement. The sedimenting entanglement is represented by a sedimenting sieve. Solvent can pass through it, but single‐chain molecules that flow into it become entangled and their flow decreases or, if permanent entanglements form, ceases entirely. With this model we are able to find the conditions under which the mass of a sedimenting entanglement remains constant, grows or decays to a stable value, grows beyond limit, or decays to the mass of a single chain. The theory is applied to the sedimentation of small concentrations of large chain molecules in solutions of small chain molecules in solutions of small chain molecules for the case in which the entanglements are long‐lived. Equations are derived which, (1) give the stable entanglement mass as a function of rotor speed and concentration and, (2) for a given concentration predict the rotor speed at which the entanglement mass grows without limit. Numerical results for small concentrations of T2 DNA sedimenting in solutions of T7 DNA are presented.
Anomalies in sedimentation. III. A model for the inherent instability of solutions of very large particles in high centrifugal fields
Authors: Schumaker Verne N. , Zimm Bruno H.
Published: December 2004

Sedimentation, diffusion, and hydrodynamic interaction are included in a simplified model for the behavior of a solution macromolecules in a centrifugal field. The model is simulated by a program on a digital computer. As the diffusion coefficient is allowed to decrease, the simulation shows that the molecules tend to cluster in high centrifugal fields. The clusters move through the solution in the direction of sedimentation in a wave‐like fashion, acquiring new molecules at the front and shedding old ones to the rear. It is suggested that this tendency to cluster could account for the loss of DNA and other very large molecules from solution which is observed to occur at high centrifugal fields.
Flow properties of high‐molecular‐weight DNA solutions: Viscosity, recoil, and longest retardation time
Authors: Massa D. J.
Published: December 2004

Viscosity η, recoil Γ, and longest retardation time τ1R were measured for buffered aqueous solution of T2 DNA (M = 1.3 × 108) and cell lysattes of Bacillus subtiles W23 (DNA M = 2 × 109) as a function of concetration, shear stress σ, and time of shear t, using a cartesian‐diver‐suspended couette flow system. For the T2 solution, η decreased with increasing σ, Γ(t) going through a maximum with t. For the B. subtiles lysates, the preponderant rheological component of which is chromatin DNA, above a critical σ, the η, Γ(t), and τ1R increased t over 15 to 45 minutes duration to values up to several times larger, indicating the formation of intermolecular aggregates. The onset of such effects and their significance in th e measurement of molecular properties by hydrodynamic means is disscussed.
The optical rotatory properties of poly‐γ‐D‐glutamic acid
Authors: Marlborough D. I.
Published: December 2004

Measurement of the optical rotatory dispersion spectra of poly‐γ‐D‐glutamic acid (obtained from Bacillus anthracis) dawn to 200 nm wavelength reveal difference between the unionized and ionized froms. The profile of the unionized polyacid shows similarities to those obtained for α‐helical polypeptides, although with displaced frequencies of the respective maxima and minima. It is suggested that the relative position and magnitudes of the Cotton effect are consistent with a helical structure such as proposed by Rydon (J. Chem. Soc., 1964, 1328). The optical rotatory dispersion spectrum of the ionized from resembles those obtained from the β‐chain from of α‐L polypeptides. From model‐building studies an extended chain similer to the β‐from would seen the most reasonable structure for the ionized poly‐γ‐acid to adopt, since the charged groups in such a conformation would be at their maximal distances from each other. Such an ordered structure for a polymer is consistent with the hypotheses put forward in the recent literature that charged polypeptides adopt ordered rather than random‐coiled conformations.
Induced circular dichroism of DNA–dye complexes
Authors: Lee Cheng H. , Chang Chiang‐Tung , Wetmur James G.
Published: December 2004

The binding of methylene blue, proflavine, and ethidium bromide with DNA has been studied by spectrophotometric titration. Methylene blue and proflavine or methylene blue and ethidium bromide were simultaneously titrated by DNA. The results indicate that all of these dyes compete for the same bindine sites. The binding properties are discussed in terms of symmetry.

The optical properties of the dye–DNA complexes have been studied as a function of DNA/dye ratio. The induced circular dichriosm due to dye–dye interaction was measured at low dye/DNA ratios for cases involving both the same dye and different dyes. A positive Cotton effect for DNA–proflavine complex may be induced at 465 mμ by eithr proflavine or ethidium bromide, whereas a netgative Cotton effect at 465 mμ may be induced by methylene blue. The limiting circular dichroism, with no dye–dye interaction, and the induced circular dichroism spectra are discussed in terms of symmetry rules.
Dilute solution of amylose in dimethylsuldoxide
Authors: Fujii M. , Honda K. , Fujita H.
Published: December 2004

Measurements of light scatting, sedimentation equilibrium, sedimentation velocity, and viscosity were carried out on fractions of native amylose in dimethylsulfoxide at 25°C. The data for statistical radius as a function of weight‐average molecular weight Mw suggested a stiff nature of this biopolymer in the solvent studied when interpreted in terms of Kirste's recent calculations with a stiff chain model. The data for sedimentation coefficient were consistent with this suggestion, and when analyzed in terms of the theory Hearst and Stockmayer for wormlike chain, a value of 233 Å2 was obtainedd for a/λ, where a is the length of a monomer unit projected on the chain axis and (2λ)−1is the persistence length of the wormlike chain. The intrinsic viscosity data gave a high a value as 0.91 for the exoponent in the Houwink‐Mark‐Sakuarada equation, in Substantial agreement with Cowie's prenious work.

We attempted to interpret these data by use of the Eizner‐Ptitsyn equation for wormlike chains, with omission of the free‐drainage term and introduction of the a/λ value obtained from sedimentation data. It was found that, except in the region of Mw above one million, the observed values were fitted well by the E‐P theory with a = 1.4 Å and (2λ)−1 = 87 Å. The disagreement in the high‐molecular‐weight region was tentatively attributed to excluded volume effect. The a value obtained suggests that the molecular conformation of amylose in dimethylsulfoxide is predominantly helical, in contrast to that of the same polymer in aqueous solutions of simple electrolyte. It was also found that a similar value of a was derived from our data for the second virial coefficient and partial specific volume if the molecule was assumed to be essentially rodlike.
Syn–Anti effects on the spatial configuration of polynucleotide chains
Authors: Olson Wilma K.
Published: December 2004

Semiempirical energy calculations have beeb performed on model nucleic acid systems to assess the preferred conformation of the rotation χ about the glycosidic linkage and also the effect of this rotation on the spatial configuration of the sugar‐phosphate chain backbone. The rotation angle ϕ˝ about bond C5′–C4′ in purine polyribonucleotides and 5′‐monoribonucleotides is found to depend on whether the conformational range of χ is syn or anti. The preferred conformation of χ in these molecules is also found to depend upon the nature of the attached base. The orientation of χ in poly rA chains is predicted to be predominantly anti, whereas in poly rG the syn conformer is expected to occur in significant proportions. The syn conformer is preferred almost exclusively in certain unusual purine polynucleotides, such as poly 8Br‐rA. It is noted that the preferred conformation of x in polynucleotides is not necessarily the same as that calculated for 5′‐mononucleotides and nucleosides. On the basis of these calculations, the influence of the orientation and nature of a purine base on the spatial configuration of a polynucleotide chain as a whole has been examined. The random coil dimensions of a syn polynucleotide chain are found to be larger than those of an anti chain as a consequence of the effect of a syn base on the local conformation of the chain skeleton. Finally, it is found that the occurrence of a syn base in an ordered polynucleotide chain may prevent the formation of normal stacking with the preceding base.
Conformational studies on guanosine nucleotides and polynucleotides. The effect of the base on the glycosyl and backbone conformations
Authors: Yathindra N. , Sundaralingam M.
Published: December 2004

Potential energy calculations have been carried out on guanosine 5′‐monophosphate and guanosine 3′,5′‐diphosphate by simultaneous variation of the rotation angles χ and ψ to assess the influence of the base on the glycosyl and the sugar–phosphate backbone conformations and their possible interdependence. The results obtained predict that guanine containing nucleotides tend to favor the syn glycosyl conformation in sharp contrast to the anti conformation found for adenine and the common pyrimidine nucleotides. This characteristic behavior of guanine nucleotides is largely a result of increased non‐bonded van der Waals' and electrostatic attractive interactions between the 5′‐phosphate and the amino group of the base. As seen previously [N. Yathindra and M. Sundaralingam, Biopolymers, 12, 297 (1973)] changes in the glycosyl conformation mainly affects the C(4′)–C(5′) bond rotations of the backbone. The most favored (χ,ψ) conformer corresponding to the global minimum both in 5′‐GMP and 3′,5′‐GDP is syn‐gg, (190°,80°) for C(2′)‐endo rings and (180°,50°) for C(3′)‐endo rings. It is noteworthy that the syn angle is different from the usually observed range of 210–260°. The next significant minimum in the (χ,ψ) energy surface corresponds to the syn‐gt conformational combination (the syn angle now in the normal range), indicating that the occurrence of the normal syn conformer induces a distortion in the backbone c(4′)‐c(5′) bond conformation from the preferred gg. These studies reveal the significant influence of the base not only on the glycosyl conformation but also on the backbone conformations of polynucleotides.
Hydration of stratum corneum
Authors: Anderson R. L. , Cassidy J. M. , Hansen J. R. , Yellin W.
Published: December 2004

A model for the hydration behavior of human stratum corneum has been developed from measurements on in vitro samples isolated in a manner which minimized tissue treatment and trauma. Water sorption/desorption rate measurements as a function of water activity, temperature, and tissue integrity are reported. These data, together with thermodynamic data (infrared and nmr results reported earlier) are consistent with a model in which rapidly sorbed/desorbed water (ca. 0.5 mg water/mg stratum corneum) is associated with (“bound” by) the tissue, while slowly sorbed/desorbed “free” water (up to 12 mg water/mg stratum corneum) is kinetically restricted and probably intracellular in location. Both equilibrium water binding and desorption kinetic data suggest structural changes of this cellular water barrier upon hydration. Evidence for hysteresis in water sorption isotherms (reported by others) could not be reproduced.
Metastable secondary structures in ribosomal RNA: A new method for analyzing the titration behavior of rRNA
Authors: Revzin Arnold , Neumann Eberhard , Katchalsky Aharon
Published: December 2004

The pH titration behavior of E. coli rRNA in the acid range has been analyzed by combining spectrophotometric and potentiometric titration data. The “simplest” model for the system, which considers as possible reactions the protonation of adenine (A), cytosine (C), and guanine (G) residues along with the opening of A·U and G·C base pairs, does not adequately account for the titration properties. It is postulated that extra reactions may occur in addition to those in the “simplest” model, and a new analytical method was developed to deal with this situation. Our approach yields the ultraviolet spectral changes which accompany the extra reactions, from which the nature of these reactions can in principle be deduced. The calculations also give, at each pH, the extents of the extra reactions as well as the extents of those reactions which comprise the “simplest” model.

We infer that in acidic RNA solutions of 0.1M ionic strength there occur at least two extra reactions, each of which involves G residues. We propose that in the pH range 6.0 ≥ pH ≥ 3.8 triple‐stranded helical sequences, presumably protonated G·C·G, are formed. These regions are replaced at lower pH by acid‐stable structures involving G·G and A·A base pairs. In solutions of lower ionic strength (I = 0.01M) no triple strands are formed, but G·G and A·A regions seem to develop even at pH values as high as 6.0. At I = 0.1M, an acid–base titration cycle between pH 7 and 2.8 is not reversible; rRNA shows true hysteresis behavior. We conclude that in ribosomal RNA's, which are generally G‐rich, guanine residues may participate in hitherto unpredicted conformations, some of which may be metastable while others are equilibrium structures.
Fluorescence correlation spectroscopy. I. Conceptual basis and theory
Authors: Elson Elliot L. , Magde Douglas
Published: December 2004

We describe a method for determining chemical kinetic constants and diffusion coefficients by measuring the rates of decay of spontaneous concentration fluctuations. The equilibrium of the system is not disturbed during the measurement. We measure the number of molecules of a specified type in a defined open volume as a function of time and compute the time course of the deviations from the thermodynamic mean concentration. The method is based on the principle that the rates of decay of spontaneous microscopic fluctuations are determined by the same phenomenological rate coefficients as those of macroscopic departures from equilibrium which result from external perturbations. Hence, an analysis of fluctuations yields the same chemical rate constants and diffusion coefficients as are measured by conventional procedures. In practice the number of the specified molecules is measured by a property such as absorbance or fluorescence which is specific and sensitive to chemical change. The sample volume is defined by a light beam which traverses the cell. As the molecules appear in or disappear from the light beam, either due to diffusion or chemical reaction, their concentration fluctuations give rise to corresponding fluctuations of the intensity of absorbed or emitted light. This paper presents the theory needed to derive chemical rate constants and diffusion coefficients from these fluctuations in light intensity. The theory is applied to three examples of general interest: pure diffusion in the absence of chemical reaction; the binding of a small rapidly diffusing ligand to a larger slowly diffusing macromolecule; and a unimolecular isomerization. The method should be especially useful in studying highly cooperative systems, relatively noncooperative systems with intermediate states closely spaced in free energy, small systems, and systems not readily subject to perturbations of state.
Fluorescence correlation spectroscopy. II. An experimental realization
Authors: Magde Douglas , Elson Elliot L. , Webb Watt W.
Published: December 2004

This paper describes the first experimental application of fluorescence correlation spectroscopy, a new method for determining chemical kinetic constants and diffusion coefficients. These quantities are measured by observing the time behaviour of the tiny concentration fluctuations which occur spontaneously in the reaction system even when it is in equilibrium. The equilibrium of the system is not disturbed during the experiment. The diffusion coefficients and chemical rate constants which determine the average time behaviour of these spontaneous fluctuations are the same as those sought by more conventional methods including temperature‐jump or other perturbation techniques. The experiment consists essentially in measuring the variation with time of the number of molecules of specified reactants in a defined open volume of solution. The concentration of a reactant is measured by its fluorescence; the sample volume is defined by a focused laser beam which excites the fluorescence. The fluorescent emission fluctuates in proportion with the changes in the number of fluorescent molecules as they diffuse into and out of the sample volume and as they are created or eliminated by the chemical reactions. The number of these reactant molecules must be small to permit detection of the concentration fluctuations. Hence the sample volume is small (10−8 ml) and the concentration of the solutes is low (∼ 10−9 M). We have applied this technique to the study of two prototype systems: the simple example of pure diffusion of a single fluorescent species, rhodamine 6G, and the more interesting but more challenging example of the reaction of macromolecular DNA with the drug ethidium bromide to form a fluorescent complex. The increase of the fluorescence of the ethidium bromide upon formation of the complex permits the observation of the decay of concentration fluctuations via the chemical reaction and consequently the determination of chemical rate constants.
α‐Glutamyl oligopeptides: Preparation by the solid‐phase method
Authors: Bonora G. M. , Toniolo C. , Fontana A. , Di Bello C. , Scoffone E.
Published: December 2004

The synthesis of the oligomeric peptides (Glu)n–Phe(NO2)–Phe (up to n = 4) by the solid‐phase method is reported. Fractionation by ion‐exchange column chromatography of the crude materials cleaved from the resin and subsequent amino acid analysis revealed that the desired peptides were obtained, although contaminated by several by‐products whose number depends on the length of peptide chain and on the experimental conditions.
Analysis of circular dichroism spectra of homopurine: Homopyrimidine DNA's for sequence information and comparison of results with heterobase DNA
Authors: Allen Fritz Schreyer , Daub Guido William
Published: December 2004

Procedures are developed which make a first neighbor frequency analysis possible from a CD spectrum of homopyrimidine: homopurine DNA's. The contribution to the CD spectrum from the various first neighbor frequencies present in homopyrimidine: homopurine‐type DNA's has been determined, and hence the CD spectrum for any DNA of this type with known first neighbor frequencies can easily be calculated. An identical analysis is presented for the determination of extinction coefficients. It is further shown that unlike the more usual heteropurine–pyrimidine DNA's a random sequence does not lead to a simplified formalism. Finally, it is concluded that the homopyrimidine: homopurine DNA's have a structure that is different from that of the more usual heterobase DNA's.

A procedure capable of determining first neighbor frequencies from a CD spectrum for heterobase and/or homopurine: homopyrimidine DNA's is described. This procedure is used to determine that there is only minimal interference between these two types of DNA in the first neighbor analysis.
Stability and thermodynamics of polyuridylic acid–deoxyadenosine complexes in aqueous neutral salt solutions
Authors: Schleich Thomas , Gould Gene R.
Published: December 2004

Using the thermodynamic analysis and methodology of Hill (Biopolymers, 12, 257 (1973)) for the treatment of optical thermal transition data the effects of various neutral salt additives on the stability and thermodynamics of the poly U–deoxyadenosine interactions that lead to the formation of triple‐stranded helical polymer–monomer complexes have been studied. In order of increasing molar effectiveness as polyU–deoxyadenosine complex stability perturbants (pH 7 and in the presence of 1 M NaCl), the various ions may be ranked: SO4−2 < Cl− < Br− < ClO4−; and (CH3)4 N+ < Li+ < Rb+ ∼ Na+ < K+ < (CH3 CH2)4 N+ < urea < Guan+ ∼ (CH3(CH2)2)4 N+. Destabilizing neutral salt additives (e.g., NaClO4) caused a decrease in the absolute magnitude of the apparent enthalpy and entropy of binding relative to the values determined in the presence of NaCl. By contrast, stabilizing additives (e.g., Na2 SO4) had the opposite effect on these parameters. Along a melting curve the apparent differential heat of complex formation calculated for the binding of deoxyadenosine to poly U in 1 M NaCl appeared to vary linearly with θ, the extent of fractional binding. For such a linear dependence it can be shown that the integral heat (usually determined calorimetrically) equals the differential heat at θ = 0.5. Correcting the apparent differential heat calculated at θ = 0.5 for ligand activity resulted in values for the integral heat of binding of deoxyadenosine to poly U in 1 M NaCl of −13 to −16 kcal/mol. Binding isotherms determined in the presence of different inorganic electrolytes could be superimposed provided that different temperatures were compared. However, the additive (CH3)4NCl, which has been shown to interact preferentially with A‐T rich regions of DNA (Shapiro, Stannard, and Felsenfeld, Biochemistry, 8, 3233 (1969)) resulted in a considerably broadened binding isotherm indicating less cooperativity.
All‐valence‐shell molecular orbital calculations on the chiroptical properties of substituted and unsubstituted 2,5‐diketopiperazine structures
Authors: Richardson F. S. , Pitts W.
Published: December 2004

The chiroptical properties of L‐3‐methyl‐2,5‐diketopiperazine (L‐alanylglycyl anhydride) are examined on a theoretical model in which the electronic wave functions are obtained from semi‐empirical all‐valence‐shell molecular orbital calculations. The INDO molecular orbital model is used to perform SCF‐MO calculations on the ground states of six conformation isomers of L‐3‐methyl‐2,5‐diketopiperazine and two chiral conformational isomers of unsubstituted 2,5‐diketopiperazine. Excited‐state wave functions are constructed in the virtual orbital‐configuration interaction approximation. The rotatory strengths, dipole strengths, oscillator strengths, and dissymmetry factors of the first eight singlet–singlet transitions for each of the eight structures are calculated and reported. Additionally, ground‐state dipole moments, net atomic charges, and the first four ionization potentials (calculated according to Koopman's theorem) are computed for each structure. The signs and the magnitudes of the rotatory strengths are found to be extremely sensitive to the conformation of the piperazine ring as well as to methyl substitution at the α carbon of the ring. Spectra–structure relationships based on the calculations reported here are discussed, and the available experimental CD data on dissymmetric 2,5‐diketopiperazine are examined in terms of our theoretical results.
The strand‐separation transition of T7 DNA
Authors: Kallay Michael , Record M. Thomas
Published: December 2004

The strand‐separation transition of T7 DNA has been investigated by temperature shift and viscosity measurements in two formamide–water solvents. The strand‐separation region is quite narrow, and follows directly at the end of the denaturation transition observed by absorbance. The kinetics of strand separation of T7 DNA are slow and complex in the strand‐separation transition. Similarities and differences in the behavior of T2 and T7 DNA in strand separation are indicated and discussed. Briefly, the time course of strand separation and the conformational changes observed in the population undergoing strand separation are similar for the two molecules. However, the transition breadths and the interval between the helix–coil transition and the strand‐separation transition differ markedly. Both DNA molecules exhibit hysteresis in the strand‐separation region. For both molecules, it appears that strand separation involves the coupled denaturation and disentanglement of the two‐stranded form found at the end of the helix–coil transition.
Studies of deoxyribonucleoproteins progressively depleted of proteins in solutions of various ionic strengths
Authors: Frisman E. V. , Sibileva M. A. , D'Iakova E. B. , Vorob'ev V. I. , Turoverova L. V.
Published: December 2004

The conformation of deoxyribonucleoprotein (DNP) from calf thymus at different stages of deproteinization was studied.

The dissociation of the first portion of histone produces no effect on the hydrodynamical and optical behavior of DNP particles. The conformational transition of a macromolecule was observed as soon as the ratio of protein to DNA ⩽ 0.9.

The effect of ionic strength on the conformation of DNP particles with high protein content was more strongly pronounced than that for DNA. On the contrary, DNP particles depleted of proteins (protein/DNA < 0.9) were found to be less sensitive than DNA to the variation of ionic strength. These data imply that the DNP molecules rich in proteins possess a superstructure that is destroyed as the protein/DNA ratio becomes 0.9.

The data were analyzed in view of current theories on various model concepts. The most probable model to describe the DNP molecule was chosen by comparing the calculated and experimentally obtained parameters. We believe that DNP is best described as a “compressed coil,” possibly including superhelical regions.
The thermal induced helix—β transition of poly(Nε‐methyl‐L‐lysine) and poly(Nδ‐ethyl‐L‐ornithine) in aqueous solution
Authors: Yamamoto Hiroyuki , Yang Jen Tsi
Published: December 2004

Uncharged poly(Nε‐methyl‐L‐lysine) (PMLL) and its isomer, poly(Nδ‐ethyl‐L‐ornithine) (PELO), in alkaline solution (pH ca. 12) undergo a helix‐to‐β transition upon mild heating at 50°C or higher in a manner similar to that of poly(L‐lysine) (PLL). The rate of conversion follows the order: PMLL < PELO < PLL. The helix can be regenerated upon cooling near zero degrees, for instance, after more than 12 hr at 2°C. At concentrations less than 0.02% the β form is intramolecular, but at higher concentrations both intra‐ and intermolecular β forms are generated. Poly(Nδ‐methyl‐L‐ornithine) (PMLO), an isomer of PLL, behaves like poly(L‐ornithine); uncharged PMLO in alkaline solution is partially helical and becomes disordered at elevated temperatures.
Crystal and molecular structure of V‐anhydrous amylose
Authors: Winter William T. , Sarko A.
Published: December 2004

The conformation and crystalline packing of V‐anhydrous amylose has been investigated by a combination of linked atom model building and X‐ray diffraction analysis. The unit cell, the P212121 space group, the left‐handed sixfold helical conformation with all O(6) in gt rotational positions, and the intrahelical O(2)‐‐‐O(3) and O(2)‐‐‐O(6) hydrogen bonds are substantially in agreement with previous studies. A new model for packing of the chains in the unit cell and the presence of crystallographic water is proposed. Packing appears to be stabilized by corner‐to‐center chain O(2)‐‐‐O(2) hydrogen bonds. The nature of the transition from the amylose–DMSO complex to Va‐amylose was considered and it is shown that the transition involves translation of the amylose chains parallel to the a and b unit cell axes with only slight changes in the orientation of the helix. No significant conformational changes result from the transition.
Crystal and molecular structure of the amylose–DMSO complex
Authors: Winter William T. , Sarko Anatole
Published: December 2004

The crystal and molecular structure of the complex of amylose with dimethyl sulfoxide has been studied by a combination of stereochemical analysis, potential energy, and X‐ray diffraction methods. The complex crystallizes in a pseudotetragonal unit cell with a = b = 19.17 Å and c (fiber axis) = 24.39 Å, with two antiparallel chains per unit cell and space group P212121. The amylose chain is a left‐handed 61(1.355) helix with three turns per crystallographic repeat. The O(6) rotational position is approximately gt. Dimethyl sulfoxide is located inside the helix with one DMSO molecule for every three glucose residues. An additional four DMSO molecules and eight water molecules each are located in the large interstices between chains, and it is the interaction of these molecules with the helix that results in the pseudotetragonal chain packing. The interstitial DMSO is the source of the previously reported additional layer lines, which are not consistent with the 8.13‐Å amylose repeat distance. The final R factor for the layers with amylose contribution to the structure factors was 0.29, while the overall R factor was 0.35. The stereochemical packing analysis provided suitable phasing models for the subsequent X‐ray refinement.
Conformational behavior of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine in water–methanol mixtures studied by 13C nmr and CD spectroscopy
Authors: Di Blasi R. , Verdini A. S.
Published: December 2004

The helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine (PHPLG) has been studied in methanol–water by CD and cmr spectroscopy. For polydisperse PHPLG, two separate peaks arising from residues in helical and random‐coil conformations are observed during the transition for both main‐chain carbons. These results are discussed and compared to those observed in the case of a polymer sample obtained by racemization of PHPLG in 0.1 M NaOH and of PHPLG samples of controlled molecular weight and dispersity. The dominant influence of the molecular‐weight heterogeneity on the double‐peak phenomenon has been verified. The linewidths and chemical shift of the 13C resonances are discussed in terms of side‐chain–main‐chain interactions and side‐chain solvation.
The nature of the helix–random coil transition of biological macromolecules attached to a surface
Authors: Dimarzio Edmund A. , Bishop Marvin
Published: December 2004

The effect of the presence of a surface on the helix–random coil transition is investigated. It is found that a grand canonical ensemble formation used previously to solve exactly the problem of a polymer between two plates can be used to solve approximately the problem of DNA near a plane surface. The formalism is applied to the homogeneous perfect‐matching model of infinite molecular weight. A crucial part of the calculation for double‐stranded molecules involves the evaluation of the entropy of the loops connecting the helical portions of the double‐stranded chains. One obtains as a measure of the configurational freedom of a loop Asi/jc where c has the following values: for a loop connecting two helical regions both off the surface c = 3/2; for a loop connecting a helical region on the surface to a helical region off the surface c = 5/2; for a loop connecting helixes both on the surface c = 4. Corresponding values for an n‐stranded molecule are c = (3n − 3)/2, c = (4n − 3)/2, c = (5n − 2)/2. In all cases, the effect of the surface is to sharpen the transition. In the case of double‐stranded molecules, the transition becomes first order. We take the view that self‐assembly of biological macromolecules can be considered as a sharp thermodynamic phase transition. Thus, the above systems become models of self‐assembling systems. They are also relevant to the problem of surface‐induced enzymatic activity.
Conformational change of the triple‐helical structure. IV. Kinetics of the helix‐folding of (Pro‐Pro‐Gly)n (n = 10, 12, and 15)
Authors: Sutoh Kazuo , Noda Haruhiko
Published: December 2004

The kinetic curves of the helix‐refolding of (PPG)n (n = 10, 12, and 15) were analyzed with an all‐or‐none model. The Arrhenius plot of the overall rate constant of the helixfolding kF showed a negative activation energy at high temperature. With the aid of a sequential model, it was concluded that the reason for the anomaly was the instability of short helices (shorter than seven helical units in a trimeric molecule), and/or the more rapid rates of helix‐folding and helix‐opening for shorter helices.

The rate constant of the formation of one helical unit composed of three tripeptides at an end of a long helix was calculated to be 102–4 sec−1. It was much smaller than that for other kinds of helices, such as an α helix (1010 sec−1) or a double helix of nucleic acids (107–9sec−1).