bluuebunny/crossref_metadata_2025 huggingface dataset:
Circular dichroism of acridine orange bound to DNA
Authors: Zama M. , Ichimura S.
Published: December 2004

The circular dichroism (CD) spectra of DNA–acridine orange (DNA–AO) complex in the visible region were measured at DNA phosphate‐to‐dye ratios (P/D) from 1 to 550. The CD spectrum of DNA–AO complex in the P/D ratio between 1 and approximately 40 consists of four components, i.e., positive CD bands centered at 510 and 480 mμ, and negative CD bands at 497 and 468 mμ. The CD bands at 510 and 468 mμ are optimum at P/D = 4, and the change of ε1 − εr with P/D suggests that both of them are induced from the interaction between dye molecules bound to adjacent DNA binding sites, each of which is composed of four nucleotides. This is supported by the fact that the values of ε1 − εr for both decrease with increasing temperature or increasing methylene blue concentration added to the complex. The negative Cotton effect at, 497 mμ is most favored at larger P/D ratio (∼8), and the suggested assignment is to the interaction between two dye molecules bound with an empty site between them. A positive Cotton effect at 480 mμ is observed at P/D ratio of less than 4 and is optimum at 1. Above P/D ratio of 40, the CD spectrum of the complex can not be resolved into its components and even at sufficiently high P/D ratio (550) the complex shows a small Cotton effect.
Kinetic equations for surface adsorption
Authors: Nossal Ralph , Ninham Barry
Published: December 2004

We investigate the time‐dependent solution of a set of equations used to approximate the binding of flexible polymers to the surface of suspended targets. The equations account, for the possibility that the first adsorption step can be a rate limiting step. Rate constants for other steps of adsorption and desorption are proportional to the number of free and occupied polymer binding sites, respectively.
Measurement of flow birefringence at very low velocity gradients
Authors: Harrington R. E.
Published: December 2004

Instrumentation and associated techniques are described for the measurement of flow birefringence and extinction angles of high molecular weight polymer systems at extremely low velocity gradients. Precision of less than one degree in the extinction angles is obtained for birefringence smaller than 10−11, based upon studies of very dilute high molecular weight DNA solutions over a range of velocity gradients from 0.1 to 3 sec−1. Extinction angles approaching 44° are also observed with at least this degree of reliability for these systems. A relatively simple method of data reduction is outlined which permits explicit correction for solvent effects and for residual instrument birefringence and background; only the latter are found to be necessary at the shear rates reported in this communication. Applicability of the techniques to other macromolecules of biological interest is discussed.
Aggregation of poly(γ‐benzyl‐L‐glutamate) in mixed solvent systems
Authors: Powers John C. , Peticolas Warner L.
Published: December 2004

The aggregation of poly(γ‐benzyl L‐glutamate) has been studied by measuring the specific Kerr constants (B/c) over a tenfold range of concentration and the intrinsic viscosities of solutions of a low molecular weight sample of the polymer in four solvent mixtures, viz., benzene–dimethylformamide (DMF), benzene–ethylene dichloride (EDC), dioxane–DMF and dixoane–EDC. Sharp changes are found in the experimentally determined quantities on the addition of small amounts of polar solvent to solutions of the polymer in either benzene or dioxane; this implies that lyotropic phase changes are occuring. The aggregation in benzene produces a birefringent, viscous solution which is probably a smeetic liquid crystal. This changes on addition of polar solvent to an aggregation involving only a few molecules; the second aggregate is most likely antiparallel. Aggregation in dioxane is antiparallel; the existence of a smectic phase is ruled out by the low intrinsic viscosities.
Helix–coil transition in heterogeneous chains. II. DNA model
Authors: Eichinger B. K. , Fixman M.
Published: December 2004

Melting curves are calculated for infinitely long DNA‐like random copolymers composed of AT and GC pairs of nucleotides. The entropy of random coil rings formed on melting is explicitly included through use of the Jacobson‐Stockmayer ring‐weighting factors. Transition curves are calculated for values of the cooperativity parameter σ in the range 10−2 ⩽ σ ⩽ 10−4. Ninety percent of the melting occurs in ca. 0.2°C for σ ⩽ 10−3 regardless of the mole fraction of GC. We conclude that observed breadths of thermal denaturation curves for native DNAs result from a superposition of essentially all‐or‐none melting of various regions of the molecule. It is argued that refined approximations to the ring‐weighting factors are probably not important when compared with the effects produced by long‐range base sequence correlations which are known to occur in native DNA.
A new approach to the study of sequence‐dependent properties of polynucleotides
Authors: Gray Donald M. , Tinoco Ignacio
Published: December 2004

A sequence‐dependent properly of any long polynucleotide can be related to the properties of a limited number of other polynucleotides. The properties of the constituent sequence subunits need not be individually known. Only the properties of a set of linearly independent sequence combinations in polymers need be known. The number of independent sequences depends on the number of neighboring bases (or base pairs) contributing to the property and on the number of different bases (or base pairs) allowed. General formulae are derived. If only nearest neighbors contribute to a property, there are 13 linearly independent single‐strand sequences with four different bases and there are 8 linearly independent double‐strand sequences with two different base pairs. The study of independent sequences in polymers should be especially useful with double‐stranded polynucleotides. It should be possible by this polymer approach to estimate nearest‐neighbor frequencies from the circular dichroism of double strands and also to investigate the relation between solution conformation and double‐strand sequence.
Theory of chromatography of macromolecules with rigid structures on hydroxyapatite columns. I. Static part
Authors: Kawasaki Tsutomu
Published: December 2004

A theory for the chromatography of rigid macromolecules on hydroxyapatite columns has been developed under the assumptions of instantaneous thermodynamic equilibrium between adsorbed phase and solution and of negligible longitudinal diffusion of macro‐molecules. In the first or static part of this theory the adsorption isotherm of macro‐molecules was studied as a function of phosphate concentration in the solvent.
Determination of molecular weight distributions and particle scattering factors of the various species of an aggregating system from light‐scattering and low‐angle X‐ray scattering data
Authors: Magar Magar E.
Published: December 2004

Several methods are presented for the determination of molecular weight distributions from light‐scattering and low‐angle x‐ray scattering data. These methods are also applicable to the experimental determination of the particle scattering factors of various aggregates provided the molecular weight distribution of the aggregates is known. The statistical analyses pertinent to these methods are appended.
On the helix–coil equilibrium in two‐ and three‐stranded complexes involving complementary poly‐ and oligonucleotides
Authors: Damle Vinayak N.
Published: December 2004

The helix–coil equilibrium in molecular complexes formed between long homopoly‐nucleotides and short complementary oligonucleotides is discussed. Each oligomer is allowed to bind to polymer(s) in an all‐or‐none fashion. The formal treatment of Lifson and Zimm is used as a basis for derivations. Approximations for long polymer(s) yield simple formulae describing the transition. The theory is applied to both a two‐stranded complex (i.e., a complex, one strand of which is a long polymer and the other of which consists of a number of short oligomers) and to a three‐stranded complex (i.e., a complex, two strands of which are long polymers and the third of which consists of a number of short oligomers). For the two‐stranded complex, simple expressions result for average quantities when the interruption constant is much smaller than unity. For the three‐stranded complex the matching and the mismatching models are considered in the case where the non‐bonded segments of polymer chains may form closed loops, and it is shown that true phase transitions occur under certain conditions. For a highly cooperative transition the slope of the melting curve is shown to be independent of the cooperativity parameter, provided that residue molar concentrations of the polymer and oligomer are of comparable magnitude. It is thus possible to obtain the enthalpy of the transition directly from the slopes of the melting curves. Some experimental results on two‐ and three‐stranded complexes are compared with the theory and yield the enthalpy and the entropy for the formation of base pairs and triplets.
Theoretical structure of the polar regions of the tropocollagen molecule
Authors: Hopfingkr A. J. , Walton A. G.
Published: December 2004

The theoretical conformations of poly (Gly‐Ala‐Glu) have been studied. This peptide was chosen as a model for the glycine led triads of the polar regions in collagen. The most favorable conformations are found to be based on the extended and folded forms of the 27 helix (27a and 27b). It is suggested that triple‐strand structures of folded 27 helices exist in the polar collagen regions, and a structural model is presented which is in accord with recent ultrastructural deformation studies. It is a necessary condition for this structure that glycine occur in the lead of the peptide triads. In regions of the collagen molecule where the primary sequence does not contain triads (e.g., in the telopeptide region), random structures based on energy minimization of peptide neighbors are considered briefly. It seems likely that such regions contain an admixture of left‐hand α, polyproline II, and 27 helix structures.
Volume changes accompanying thermal denaturation of deoxyribonucleic acid. II. Denaturation at alkaline pH
Authors: Chapman R. E. , Sturtevant J. M.
Published: December 2004

The change in apparent molal volume ϕ of DNA on thermal denaturation in carbonate buffer at pH 11.0 has been determined by the dilatometric method. It was found that ϕ increases sigmoidally during the helix–coil transition. Several methods, including a colorimetric technique that closely simulates the conditions used in the dilatometric experiments, were employed to estimate the protons lost by the DNA during the transition. These measurements indicated that the extent of the proton loss depends on the counterion present, increasing in the order Li+ < Na+ < K+ < Cs+. The major part of the volume changes observed during the denaturation is due to the volume changes expected to accompany the transfer of protons from the bases guanine and thym ne to carbonate ions. As has been previously reported for the denaturation of DNA at neutral pH, the volume change directly due to the change in shape of the polymer molecules is so small as to be experimentally undetectable.
Location of proline derivatives in conformational space. I. Conformational calculations; optical activity and NMR experiments
Authors: Madison Vincent , Schellman John
Published: December 2004

In order to develop methods of analysis applicable to the determination of the conformation of biological polymers in solution, a series of proline derivatives was studied. The steric constraints of the pyrrolidine ring limit these compounds to a relatively small set of conformations. This set was further reduced by eliminating conformations with large computed conformational energy. Computations revealed that the conformational energy of the proline derivatives fits into one of three classes, depending on the bulk and the polarity of the C‐terminal group. Three analogous classes of optical activity were observed. The optical activity data were analyzed in terms of conformations computed to be of low energy. In some cases qualitative theoretical considerations enabled molecular groups to be located. For example, solvent‐dependent isomerization of the carboxyl hydrogen of N‐acetyl‐L‐proline was detected. Nuclear magnetic resonance provided an experimental measure of the fraction of molecules which had cis unsymmetrically‐substituted tertiary amide groups. This information aided and confirmed the other measures of molecular conformation.
Density gradient proportionality constants for a number of aqueous binary solutions
Authors: Ifft James B. , Martin William R. , Kinzie Kathleen
Published: December 2004

A computer program, based upon the method of Trautman, has been developed to calculate density‐gradient proportionality constants, β0, as a function of density for any salt for which density and activity coefficient data are available. Results are given for twenty 1:1 electrolytes at 25°C. These salts are the chlorides, bromides, iodides, and nitrates of the five alkali cations. The program is available for use for any other salt and for a variety of temperatures if the necessary data can be found or measured. Between six and eleven centrifuge runs at different densities were performed fur each of seven of these salts experimentally to determine β0. In general, the experimental and theoretical values agree within 3% except at the extremes of density. This demonstrates the validity of the computer program and is the first extensive demonstration that the thermodynamic calculation of density gradients is correct. Five new quadratic relationships between refractive index and density are given.
Quantitative flow dichroism. I. Correction for disorientation in a solution of rods
Authors: Mayfield John E. , Bendet Irwin J.
Published: December 2004

Flow dichroism suffers from two ambiguities which have prevented it from being a useful analytical technique. One is imperfect particle orientation, and the other is the unknown importance of form dichroism. This paper presents a method for calculating from experimental data the dichroism which would be observed from a solution in which all rods were aligned parallel to one another. The procedure utilizes anisotropic light scattering as an independent measure of particle orientation and requires only that the solute particles may be approximated by thin rods.
Quantitative flow dichroism. II. Form dichroism at ultraviolet wavelengths
Authors: Mayfield John E. , Bendet Irwin J.
Published: December 2004

Form dichroism has been predicted to make an important contribution to the dichroic spectra of rod‐shaped macromolecules. Ultraviolet flow dichroism experiments on tobacco mosaic virus and bacteriophage fd in solvents of different refractive indices were unable to detect the phenomenon, indicating that for these viruses form dichroism is much less important than had been postulated.
Ionic polysaccharides. III. Dilute solution properties of hyaluronic acid fractions
Authors: Cleland Robert L. , Wang John L.
Published: December 2004

Molecular weights by osmometry (M̄n), light scattering (M̄w), and sedimentation‐diffusion (MsD) were determined for selected fractions and unfractionated samples of hyaluronic acid in the molecular weight range 3 × 104−1.7 × 106. For the determination of MsD from the sedimentation coefficient s, a calibration procedure based on the data of Laurent, Ryan, and Pietruszkiewicz gave the following relations in 0.2M NaCl: log (s−1)0 = 14.681 − 0.413 log MsD and log D0 = −3.828 − 0.568 log MsD, where subscript, zero refers to zero concentration and D is the diffusion coefficient. The average Mandelkern‐Flory parameter β in 0.2M NaCl is 3.0 × 106. Data for the intrinsic viscosity [η] may be fitted for M > 105 by [η] = K′Ma, where K′, a are in 0.2M NaCl, 0.0228, 0.816; in 0.5M NaCl, 0.0318, 0.777; in 0.1 M HCl, 0.0279, 0.763, respectively. Below M = 105, [η] appears to fall below the values calculated, possibly due to non‐Gaussian behavior of short chains. The second virial coefficient A2 in 0.5M NaCl approaches the ideal Donnan value, decreasing slightly with increasing molecular weight. The friction parameter P is about 20% smaller than that of uncharged polymers of similar dimensions. The flexible coiling nature of this polymer is confirmed.
Mechanochemical study of wet‐spun lithium‐DNA fibers
Authors: Rupprecht A.
Published: December 2004

Uniform LiDNA fiber specimens of nearly 20 m length have been prepared with a wet‐spinning method developed by the author. Samples immersed in the spinning bath (80% ethyl alcohol containing 0.4M LiCl) have been subjected to mechanochemical study involving stretching, relaxation, and contraction measurements. A special technique was developed to transfer the sample from the Teflon‐coated cylinder used in spinning to the sample column of the mechanochemical apparatus without stretching or removing the sample from the spinning bath. Force–strain curves of samples consisting of two fiber bundles showed an initial region of low slope followed by a region of high slope and a second region of low slope up to rupture. Some thicker specimens showed an aging effect which abolished the initial low‐slope region and was interpreted as indicative of crystallization. Force–strain curves of two‐bundle samples showed a strong influence of temperature with a complete loss of tensile strength of the LiDNA fibers in the spinning bath at about 55°C. Furthermore, samples at zero strain exhibited a contractile force when subjected to temperatures above about 40°C; the contractile process was pronounced with samples kept above 48°C. On contraction these samples obtained a zero‐force length 20–30% of the original. These data are taken as evidence for a helix‐to‐coil transition occurring in the DNA, the low melting temperature being caused by the chemical influence of the ambient aqueous alcohol–LiCl bath.
Diffusional boundary spreading in the ultracentrifuge
Authors: Weiss George H. , Dishon Menachem
Published: December 2004

A common approximation for deriving solutions to the Lamm equation is to neglect diffusion. This paper presents a singular perturbation technique that allows one to estimate the band spreading due to nonzero diffusion coefficient. We illustrate the general mathematical technique by its application to sedimentation when pressure effects are important. Comparison of the approximate solution with accurate numerical solutions shows that the relative errors are of the order of 1% both for concentration and concentration gradient for parameters of chemical interest.
Conformation of poly‐L‐tyrosine in trimethyl phosphate solution
Authors: Damle Vinayak N.
Published: December 2004

Absorption, circular dichroism (CD), and optical rotatory dispersion (ORD) measurements were carried out on poly‐L‐tyrosine in trimethyl phosphate solution over the spectral range 185–600 mμ. There is evidence in the CD spectrum for side chain‐side chain interactions in poly‐L‐tyrosine. ORD and CD data in dimethylformamide and pyridine closely parallel those in trimethyl phosphate, indicating a similarity in conformation of the polymer in all three solvents. In the polarized infrared spectrum both position and polarization of amide A, I, and II bands are characteristic of α‐helical polypeptides. Bands corresponding to side chain also exhibit dichroism, suggesting that the side chains are not randomly oriented. Viscosity and light‐scattering studies are consistent with α‐helical structure for the polymer that, remains rigid over a temperature range of 15–50°C and becomes somewhat flexible at higher temperatures. Optical rotatory properties were found to vary gradually and continuously with temperature over the range of −30 to +100°C. This suggested that all three electronic transitions of tyrosyl side chain are optically active, and that the side chains have some freedom of motion that decreases with decreasing temperature, disappearing only at about −30°C.
Characterization of acid‐denatured DNA by low‐angle light scattering
Authors: Krasna Alvin I. , Dawson Jeffrey R. , Harpst Jerry A.
Published: December 2004

Low‐angle light scattering results reported previously demonstrated that measurements on high molecular weight native DNA must be made at angles below 30° in order to obtain correct molecular weights. Earlier light‐scattering data obtained on denaturated DNA at angles above 30° showed no change in molecular weight upon denaturation, even though other techniques clearly showed that strand separation occurred. This paper reports low‐angle measurements on solutions of calf thymus and T7 DNA denatured under acidic conditions. The results demonstrate that a halving of molecular weight consistent with strand separation is detected by light scattering only when low‐angle data are used to obtain correct molecular weights for native material. As expected from theoretical considerations, the scattering from denatured DNA is a linear function of sin2(θ/2), where θ is the angle of observation. This result shows that anticipated experimental artifacts have no significant effect on the low‐angle measurements and demonstrates that the curvature in the scattering envelope observed for native DNA below 30° is an inherent property of the native molecule.
Low‐angle light‐scattering studies on alkali‐ and heat‐denatured DNA
Authors: Krasna Alvin I.
Published: December 2004

The molecular weight of native DNA is shown to decrease by at least a factor of two on denaturation by heat or alkali. This result is obtained only if low‐angle (<30°) light‐scattering measurements are used. High‐angle measurements (>30°) do not reveal a decrease in molecular weight on denaturation due to the incorrect value for native DNA. The dn/dc value for both native and denatured DNA is 0.166 ml/g ± 0.003 ml/g. Methods are described for the clarification of native and denatured DNA solutions for light scattering by the use of membrane filters.
Potentiometric titration of poly‐S‐carboxymethyl‐L‐cysteine in aqueous NaCl solution
Authors: Makino Shio , Sugai Shintaro
Published: December 2004

pH titration measurements of poly‐ S‐carboxymethyl‐L‐cysteine were undertaken in the aqueous Nacl solution in relation to the β form–random coil transition. The titration curves show a marked molecular weight dependence because of the shortened chain length of materials. Comparison of the optical rotatory dispersion parameter a0 with the titration curve reveals that the titration curve apparently reflects a β structure–random coil transition. The β form of this polymer is assumed to be an intramolecular β form, rather than a β structure stabilized by an intermolecular hydrogen bond, at least in the polymer concentration range considered here. The standard free energy change per amino acid residue for the transition from un‐ionized random coil to un‐ionized β form is estimated to be about −750 cal/mole residue in the range of 0.005–0.2M NaCl concentration.
Optical activity of aromatic chromophores. I. o, m, and p‐tyrosine
Authors: Hooker Thomas M. , Schellman John A.
Published: December 2004

The optical activity and the conformational energy of the amino acids tyrosine, o‐tyrosine, and m‐tyrosine have been calculated as a function of molecular conformation. A new graphic technique, rotatory strength–conformational energy maps, was developed for the presentation of these calculations. Experimental circular dichroism spectra were determined by utilization of a new experimental technique that involves complete computer control of a Cary spectropolarimeter. This permitted repetitive scanning with signal averaging over extended time periods and resulted in a greatly enhanced signal to noise ratio. On the basis of these calculations, it, was concluded that the Kirkwood “coupled oscillator” mechanism is capable of explaining the observed optical activity of the aromatic chromophores of the molecules that were investigated.
The influence of single‐strand breaks on the kinetics of denaturation of DNA
Authors: Hoff A. J. , Blok Joh.
Published: December 2004

The influence of single‐strand breaks on the kinetics of the relaxation of DNA in a solution of low ionic strength has been investigated by a temperature jump method. The relaxation of DNA after a jump of 0.7 °C in the melting region has been monitored by measuring the extinction at 260 nm. For essentially monodisperse T4 DNA (M = 130 × 106) two distinct relaxation times have been observed, that depend markedly on the initial extent of denaturation 1 − θ. The larger relaxation time decreases from 450 sec to about 300 sec, the smaller one from 55 see to 30 when 1 − θ increases from 0.03 to about 0.8. The dependence of these relaxation times on the average number of single‐strand breaks per molecule (p) appears to be very small up to p = 100. However, the relative contribution of the slow process decreases sharply when p increases from 0.6 to 30 and remains nearly constant for larger p. The observations are discussed in the light recent theories of the kinetics of denaturation.
Electro‐optic scattering studies on deoxyribonucleic acid
Authors: Jennings B. R. , Plummer H.
Published: December 2004

Measurements have been made of the intensity of light scattered from aqueous solutions of calf thymus DNA with and without the application of electric fields. For fields approaching 150 V/cm and frequencies below 2.5 KHz, changes (ΔI) of up to 10% in the residual scattered intensity were observed. In agreement with previous dielectric and electric birefringence measurements, a low frequency dispersion of ΔI was observed, from which a rotary diffusion constant (D) of 1200 s−1 was determined. Interpreting the electric field data in terms of the classical dipolar orientation theory led to values of 2.4 × 10−25 cm (7.4 × 10−14 esu) and 4.3 × 10−25 cm (13 × 10−14 esu) for the permanent dipole moment and the anisotropy of the electric polarisabilities respectively. Furthermore the permanent dipole moment was along the major molecular axis and the particles orientated in the field as rigid entities. The zero field data indicated a molecular shape which was not rodlike but corresponded to the Kratky‐Porod “stiffness” parameter of x = 24 for the wormlike coil model. Although curved, the molecules appeared to orientate in low‐intensity electric fields as rigid, but not rodlike molecules. The implications of this on recent discrepancies in D determined by two or more dynamic relaxation methods is briefly discussed.
Studies on bacteriophage MS2. VIII. Evidence for dimer formation of MS2 RNA by reaction with formaldehyde at acidic pH
Authors: Slegers H. , Fiers W.
Published: December 2004

Reaction of 27 SMS2 RNA with formaldehyde normally results in an unfolded, 13.4 S form. At acidic pH, however, and under the proper ionic conditions, a compact component sedimenting at 36–40 S was obtained. The molecular weight of this species corresponds to a dinner. The formaldehyde concentration was not critical, and approximately the same number of base pairs had been opened in the compact and in the unfolded form. Presumably dimers, which had been specifically formed under defined conditions, were stabilized by formaldehyde‐induced crosslinks. Similar dimers were formed by 16 S and by 23 S ribosomal RNA, but not by tRNA.
Buoyant density and solvation of magnesium DNA
Authors: Vijayendran B. R. , Vold R. D.
Published: December 2004

The buoyant density of T‐4 DNA was determined by equilibrium sedimentation in a density gradient, of mixed solutions of cesium and magnesium chlorides and bromides. The preferential hydration was calculated from these data, allowing appropriately for the exchange equilibrium of DNA with Cs+ and Mg++ ions. The charge and intrinsic solvation of the counterions were found to have no appreciable effect on the hydration of the DNA, the extent of solvation depending only on the thermodynamic, activity of the water. Various reasonable hypotheses are discussed to account for these results.
Theory of interaction of polymer and small molecules which can aggregate in solution
Authors: Damle Vinayak N.
Published: December 2004

The theory of interaction of small molecules with polymers is extended to the case where the small molecules can aggregate in solution to form dimers, trimers, etc., and where the aggregates can also interact with the polymer. The secular equation is found to be identical in form with that obtained for the binding of nonaggregating monomer to the polymer. Thus, all formulas derived for the latter case apply to the present one also, except that, now the concentration of the free monomer is the relevant factor. It is shown how the experimental data can be analyzed by using information on the molal activity coefficients of the small molecules. As an illustration these formulas are applied to data on the interaction of purines and nucleosides with poly(uridylic acid) in concentrated solutions.
Computation of equilibrium constants for the association of two different monomer units from weight‐average molecular weight data
Authors: Steiner R. F.
Published: December 2004

A method is developed for computing the equilibrium constants for the association of two different monomers from weight‐average molecular weight data.
Dielectrophoresis of macromolecules
Authors: Eisenstadt Maurice , Scheinberg I. Herbert
Published: December 2004

Dilute solutions of rigid helical macromolecules with permanent dipole moments have been studied with dielectrophoresis. The polymers used were poly‐γ‐benzyl‐L‐glutmate and poly‐n‐butyl isocyanate, both fractions of average molecular weight 120,000. In this phenomenon dipolar molecules migrate in an inhomogeneous electric field towards the region of maximum field strength. The field gradient is produced by a 10‐μm diameter Pt wire serving as the inner electrode of a cell, and a 2.5‐mm diameter cylinder as the outer electrode. An equilibrium exponential concentration gradient is achieved within a few wire radii of the inner electrode in a matter of minutes, making both kinetic and equilibrium measurements feasible. The concentration gradient is monitored by measuring the change in capacitance ΔC of the cell from its value for a uniform solute concentration. The time dependences of ΔC for the build‐up of the concentration gradient towards the equilibrium value, and the decay to a uniform concentration after the field is removed have been calculated, using a frictional coefficient and a Boltzmann factor, β1, as the sole adjustable parameters.

For low voltages (β1 small), the measured build‐up and decay are completely symmetrical, in agreement with theory, and yield the same frictional coefficient. For larger β1, the build‐up is faster, reflecting a reduced frictional coefficient due to partial alignment of the long axes of the polymers in the direction of migration. In either case, the decay determines a diffusion constant of randomly aligned molecules, identical to classical diffusion measurement.

The value of ΔC at equilibrium, for β1 small, determines μ2F2, where μ is the dipole moment and F is the internal field at the polymer. Combined with a classical dielectric constant measurement, which gives μ2F, both μ and F may be determined, independent of assumptions about cavity shapes.

Dielectrophoresis works in alternating as well as constant fields, provided the dipolar orientation can follow the field reversals. The dispersion of dielectrophoresis with frequency is a sensitive measure of the molecular‐weight distribution of a given sample.
A carbon‐13 magnetic resonance study of the helix–coil transition in polyuridylic acid
Authors: Govil Girjesh , Smith Ian C. P.
Published: December 2004

The temperature‐dependent conformations of poly(U) in 0.5M CsC1 have been studied by carbon‐13 nuclear magnetic resonance. The transition from random coil to an ordered structure results in broadening of lines in the 13C spectra, due to intramolecular 1H–13C dipolar interactions and restricted motions in the ordered state. Changes in the chemical shifts suggest that the bases are interacting below the transition temperature. The random coil form shows conformation preferences for internal rotation about C4′–C5′, C5′–O5′, and C3′–O 3′ bonds. The statistical randomness of the coil arises mainly because of flexibility about O–P bonds. The results are analyzed in conjunction with theoretical calculations and light‐scattering data.
Transient electric birefringence of T‐even bacteriophages. I. T4B in the absence of tryptophan and fiberless T4 particles
Authors: Greve J. , Block Joh.
Published: December 2004

Measurements of the electric birefringence of suspensions of T4B in the absence of tryptophan and of fiberless T4 particles show that both kinds of particles are hydrodynamically equivalent. Their rotational diffusion coefficients corrected to 25°C and water viscosity (D25,w) are 280 ± 9 sec−1 and 295 ± 10 sec−1, respectively. These corrected rotational diffusion coefficients are almost independent of buffer concentration and temperature. The sedimentation coefficient (s20,w) of T4 B is equal to 1023 ± 12 S, a value which is likewise independent of buffer concentration.

By analysis of the field strength dependence of the steady‐state birefringence and by reversing pulse experiments it could be shown that the orientation in an electric field is largely due to a permanent dipole moment. This dipole moment is somewhat dependent on buffer concentration and amounts to about 24,000 debye for T4B and 95,000 debye for fiberless T4. An approximate calculation shows that the difference in dipole moment may be ascribed to positive charges on the fiber tip (at least ten per fiber), to negative charges along the fiber or (and) positive charges on the fiberless particle at those places where the fibers are attached in normal particles.
Conformational characteristics of dApdA, dApdT, dTpdA, and dTpdT from energy minimization studies
Authors: Thiyagarajan P. , Ponnuswamy P. K.
Published: December 2004

The conformational characteristics of the deoxydinucleoside monophosphates with adenine and thymine bases in all possible sequences, namely, dApdA, dApdT, dTpdA, and dTpdT have been studied using an improved set of energy parameters to calculate the total potential energy and an improved set of energy parameters to calculate the total potential energy and an improved version of the minimization technique to minimize the total energy by allowing all seven dihedral angles of the molecular fragment to vary simultaneously. The results reveal that the most preferred conformation in all these units usually corresponds to one of the four helical conformations, namely, the A‐DNA, B‐DNA, C‐DNA, and Watson‐Crick DNA models. These helical conformations differ in energies by about 3 kcal/mol with respect to one another. The conformations which could promote a loop or bend in the backbone are, in general, less stable by about 3.5 kcal/mol with respect to the respective lowest‐energy helical conformation. The results indicate that there is a definite influence of bases and their actual sequences on the preferred conformations of the deoxydinucleoside monophosphates. The lowest‐energy structure, although corresponding to one of the four helical conformations, differ with the type of the deoxydinucleoside monophosphate. Good or reasonable base stacking is noted in dApdA and dTpdA with both C(3′)‐endo and C(2′)‐endo sugars and in dApdT and dTpdT with only C(3′)‐endo sugar. The inversion of the base sequence in deoxydinucleoside monophosphates alters the order of preference of low‐energy conformations as well as the base‐stacking property of the unit. The paths linking the starting and final states in the (ω′, ω) plane show interesting features with regard to the energy spread, thus providing insight into the path of conformational movement ofthe molecule under slight perturbation. The stabilities of the A and B forms, including the internal energies of the C(3′)‐endo ans C(2′)‐endo sugar systems, indicate that for dTpdT the B → A transition is less probable. For dApdA, dApdT, and dTpdA this transition is probable in the same order of preference. We propose that the T‐A sequence in the polynucleotide chain might serve as the site accessible for B ⇄ A transitions. The theoretical predictions are in good agreement with the experimental observations.
Prediction of β‐sheets in immunoglobulin chains. Comparison of various methods and an expanded 20 × 20 table for evaluation of the effects of nearest‐neighbors on conformations of middle amino acids in proteins
Authors: Wu Tai Te , Szu Shousun C. , Jernigan Robert L. , Bilofsky Howard , Kabat Elvin A.
Published: December 2004

The extraordinarily large number of immunoglobulins renders them an intriguing class of molecules for attempts to predict their conformations. The predictive method applied, using a 20 × 20 table of the observed effects of nearest‐neighboring amino acids on the conformation (Φ,Ψ angles) of the middle residue in known proteins, indicates positions of tri‐peptides that tend to break α‐helices or regular β‐sheets. This 20 × 20 table is derived from data on 19 proteins, as compared with the earlier version based on 12 proteins, and includes a separate listing of residues of β‐turns that have helical Φ,Ψ values. Secondary conformations predicted by methods of Chou and Fasman, Lim and Burgess, Ponnuswamy, and Scheraga have also been compared; for all three methods, wrong predicitons of residues in β‐sheet conformation exceed correct ones. Better predictions are obtained when there is agreement with two or three of the methods. If there is consistent overprediction of β‐structure, as with the Chou and Fasman method, the use of the β‐sheet‐breaking tripeptides can improve pre‐dictability somewhat.
Synthesis of polymeric models of elastin: Polyhexapeptides and an insoluble, hybrid cross‐linked polypeptide
Authors: Okamoto K. , Rapaka R. S. , Urry D. W.
Published: December 2004

The polymer of the hexapeptide sequence, Val‐Ala‐Pro‐Gly‐Glu‐Gly, was synthesized and demostrated of exhibit a reversible, pH‐dependent coacervation in low‐pH aqueous solution. In addition, the synthesis of an insoluble, hybrid, cross‐linked polypeptide matrix is described. The cross‐linking was achieved in the coacervate state during flow orientation of the polymers. The chemical means of covalent cross‐linking was intermolecular primary amide bond formation between the lysyl side chains in one polypentapeptide unit and the glutamyl side chains in another polyhexapeptide unit. The carboxyl activating reagent was a water‐soluble carbodiimide. The key intermediates in the syntheses, the hexamers and their high polymers, were analyzed by carbon‐13 magnetic resonance to verify the correctness of synthesis and to obtain information on conformation.
Analysis of the 1H‐NMR spectra of ferrichrome peptides. II. The amide resonances
Authors: Demarco Antonio , Llinás Miguel , Wüthrich Kurt
Published: December 2004

The high‐resolution 1H‐nmr study of the ferrichrome cyclohexapeptides, in d6‐DMSO solutions, has been extended to the amide NH spectral region. A total of ten diamagnetic analogues of ferrichrome that differ in the coordinated metal ion (Al3+, Ga3+ or Co3+), the primary structure, the nature of the bidentate hydroxamate moiety, or the isotope compositions (14N, 15N) have been investigated. The 3JαNH values reflect regiorous conformational isomorphism throughout the complete suite of analogues, quite independent of the residue occupancy of each site. Totally resolved amide multiplets have been obtained in most cases and the four‐line (doublet of doublets) appearances of glycyl NH resonances has been observed for the first times; these data enabled stereospecific assignment and accurate analysis of the NH‐CαH proton spin systems. The high resolution was made possible by the use of a suitable spectral deconvolution shceme at 360 MHz. The fine structure, extraordinarily well displayed in the 15N‐peptide spectra, provides a series of parameter values whose consistency has been checked by computer simulation. Since the crystallographic structure for two of the ferric peptides is known to 0.002‐Å resolution, a 3J vs θ correspondence could be confidently established. A Karplus curve was derived from the combined x‐ray and nmr data:

It is suggested that seriously nonplanar amides can exhibit 3JαNH values higher than predicted by the ferrichrome curve.
Solution properties of synthetic polypeptiedes. XXI. Solvent effect on the helix‐coil transition of poly(e‐carbobenzoxy L‐lysine)
Authors: Nishioka Noboru , Maekawa Akio , Teramoto Akio
Published: December 2004

Helix‐coil transitions of poly(ϵ‐carbobenzoxy L‐lysine) in mixtures of dichloroacetic acid and 1,2‐dichloroethane were investigated by optical rotatory dispersion (ORD) measurements. The ORD data were analyzed according to the statistical mechanical approaches developed by Sayama et al. (1970) (Ref. 10) and by Karasz and Gajnos (1973) (Ref. 4) to obtain the enthalpy chage associated with the unfolding of helix in the inert solvent 1,2‐dichloroethane, ΔHo, and that for the solvation of the peptide backbone with the dichloroacetic acid dimer, ΔHa. The results were: ΔHo = −(340 ∼ 620) cal/mol and ΔHa = ‐(2.4 ∼ 3.6) kcal/mol. These values are favorably compared with those for poly(γ‐benzyl L‐glutamate) and poly(β‐benzyl L‐aspartage) in the same solvent system. On the other hand, the equilibrium constant for the solvation and hte cooperativity parameter in the inert solvent 1,2‐dichloroethane depended appreciably on the chemical structure of hte side chain. In terms of the Zimm‐Bragg parameter, s, which varied from 1.3 to 1.7 with polypeptied species, the helices of these three polypeptieds are far from complete even in the typical helix‐supporting solvent 1,2‐dichloroethane.
Interaction of metal ions with nucleic acids and related compounds. II. Studies on Au(III)‐nucleic acid system
Authors: Pillai C. K. S. , Nandi U. S.
Published: December 2004

The nature of interaction of Au(III) with nucleic acids was studied by using methods such as uv and ir spectrophotometry, viscometry, pH titrations, and melting‐temperature measurements. Au(III) is found to interact slowly with nucleic acids over a period of several hours. The uv spectra of native calf‐thymus DNA 9pH 5.6 acetate buffer containing (0.01MNaCIO4) showed a shift in λ max to high wavelengths and an increase in optical density at 260 nm. There was a fourfold decrease in viscosity (expressed as ηsp/c). The reaction was faster at pH 4.0 and also with denatured DNA (pH 5.6) and whole yeast RNA (pH 5.6). The order of preference of Au(III) (as deduced from the time of completion of reaction) for the nucleic acids in RNA > denatured DNA > DNA. The reaction was found to be completely reversible with respect KCN. Infrared spectra of DNA‐Au(III) complexes showed binding to both the phosphate and bases of DNA. The same conclusions were also arrived at by melting‐temperature studies of Au(III)‐DNA system. pH titrations showed liberation of two hydroxylions atr= 0.12 [r= moles of HAuCl4added per mole of DNA‐(P)] and one hydrogen ion atr= 0.5. The probable binding sites could be N(1)/N(7) of adenine, N(7) and/or C(6)O of guanine, N(3) of cytosine and N(3) of thymine.

DNAs differing in their (G = C)‐contents [Clostridium perfingensDNA(G = C, 29%), salmon sperm DNA (G + C, 42%) andMicrococcus lysodeikticusDNA(G + C, 29%), salmon sperm DNA (G = C, 72%)] behaved differently toward Au(III). The hyperchromicity observed for DNAs differing in (G + C)‐content and cyanide reversal titrations indicate selectivity toward ( A + T)‐rich DNA at lw values ofr. Chemical analysis and job's continuous variation studies indicated the existence of possible complexes above and belowr= 1. The results indicate that Au(III) ions probably bind to hte phosphate group in the initial stages of the reaction, particularly at low values ofr, and participation of the base interaction also increases. Cross‐linking of the two strands by Au(III) may take place, but a complete collapse of the doulbe helix is not envisaged. It is probable that tilting of the bases or rotaiton of the bases around the glucosidic bond, resulting in a significant distrotion of the double helix, might take place due to binding of Au(III) to DNA.
Magnesium binding to yeast ribosomes
Authors: Walters J. A. L. I. , Van Os G. A. J.
Published: December 2004

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

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