bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polynucleotides. XIII. Stoichiometric and Thermodynamic Studies of Polynucleotide Helices with Non‐Complementary Residues
Authors: Lomant A. J. , Fresco Jacques R. 
Published: December 2004

AbstractStoichiometry and thermodynamic properties of polyadenylate–polyuridylate helices containing varying proportions of near‐randomly distributed non‐complementary uridine residues were charactrized from an analysis of their mixing curves and melting profiles measured at 259 nm and at appropriate longer wavelength isochromic points. The noncomplementary residues in this homopolymer–copolymer system (in which the homopolymer has the capacity to readjust with respect to the residues with which it is in opposition) show absolute preference for an extrahelical conformation even when situated in … AAUAA … sequences and must occur therefore as single loops. As the frequency of extrahelical residues in creases, the electrostatic energy of these complexes becomes greater, and is particularly severe for the three‐stranded helices. Thus, an adenyl‐ate‐uridylate copolymer containing 35.2 mole percent uridine residues does not form a three‐stranded complex with polyuridylate even in 0.7M Na+at O°C. The imperfections introduced into the helix lattice by extrahelical residues decrease the cooperativity of thermal denaturation as well as Tm. However, for the helices with extrahelical residues in low frequency (∼1 per helix turn) only small increases in concentration of charge‐neutralizing ions are required to bring Tm to the level of their perfect analogs. Two‐stranded helices with a higher density of extra helical residues (∼5 per helix turn) show [Na+] dependence of Tm characteristic of perfect three‐stranded helices. These findings together with the absence of an effect of these imperfections on the hypochromicity per base‐pair suggest only minimal disruption of helix continuity or distortion of stacking interactions that normally in volve the base pairs or triplets.
The application of surface tension measurements to the study of conformational transitions in aqueous solutions of poly‐L‐lysine
Authors: Neumann A. W. , Moscarello M. A. , Epand R. M. 
Published: December 2004

AbstractThe change in surface tension of solutions of poly‐L‐lysine in water has been studied as a function of temperature at various pH values. The changes at various temperatures have been correlated with changes in the circular dichroic spectra reflecting conformational change. In addition to the major transition at 50°C attributed to the conversion of the α‐helical → β conformation, two other transitions have been observed at 30°C and 80°C.A minimum in the surface tension value was observed at pH 10, near the pK value for poly‐L‐lysine. It was concluded that at this pH the concentration of hydrophobic groups at the surface was a maximum.
An X‐Ray diffraction study of poly‐L‐ornithine hydrobromide
Authors: Suwalsky M. , De La Hoz L. 
Published: December 2004

AbstractAn X‐ray study has been made of the synthetic polypeptide poly‐L‐ornithine hydrobromide to investigate whether, like the chemically related polypeptides poly‐L‐lysine and poly‐L‐arginine hydrochlorides, it can undergo conformational changes merely from variations in its degree of hydration. X‐ray powder and fiber photographs of specimens with from half up to about three molecules of water per ornithine residue show features that suggest a “cross‐β‐pleated‐sheet” structure. Each pleated sheet is formed from parallel chains and the sheets are piled up along the b axis. The spacings, which do not vary appreciably with hydration, can be satisfactorily indexed in terms of an orthogonal unit cell with a = 4.60 Å, b = 30.2 Å, and c = 6.64 Å. These dimensions are shown by models to be compatible with the proposed structure. Removal of the last half molecule of water results in a very diffuse pattern but on rehydration the sharp pattern reappears. Specimens containing four to nine molecules of water per residue show a quite different pattern. Reflections other than equatorial are absent in oriented diagrams except for a 5.4 Å diffuse streak across the meridian which is suggestive of an α‐helical structure. Increasing the relative humidity from 86% to about 100% causes the a axis of the hexagonal unit cell to increase from 14.7 Å to 15.3 Å. On drying, the β structure reappears once again. These conformational changes are very similar to those observed in poly‐L‐lysine hydrochloride except that the latter shows a more stable α‐helical form. This difference may be explained in terms of stabilizing hydrophobic interactions between side chains, since ornithine has a shorter side chain than lysine.
Studies on the bacteriophage MS2. XXIV. Hydrodynamic properties of the native and acid MS2 RNA structures
Authors: Slegers H. , Clauwaert J. , Fiers W. 
Published: December 2004

AbstractThe molecular weight of native 26.6S MS2 RNA, of acidic 53.1S MS2 RNA and of formaldehyde‐treated 36.1S MS2 RNA was determined by light‐scattering studies. The three forms examined correspond to monomers. Also νv values were determined, and in conjunction with our previous estimates for S20,W and [η], led again to the conclusion that formaldehyde‐cross‐linked 37S MS2 RNA is a monomer. On the basis of the experimentally observed RG, [η], S20,W, and νv values, and taking a prolate ellipsoid as a model, the hydrodynamic volume, the solvation water and the axial ratio could be deduced for the three conformations. In the “native” 26S form the RNA occupies only 8.2% of the hydrodynamic volume. The formation of the 36S and the 53S structures correspond largely to a loss of solvation water.
Theory of oligonucleotide stabilization. I. The effect of single‐strand stacking
Authors: Appleby David W. , Kallenbach Neville R. 
Published: December 2004

AbstractCertain theoretical difficulties present in the analysis of thermal transition properties of short complementary double‐stranded RNA oligomers can be resolved in part by introducing the stability of the component single‐stranded systems explicitly into the model. The stability constant S of the usual theories is redefined so as to contain double‐stranded pairing (τt) and single‐stranded stacking (ρ) contributions, and we analyze the statistics of two experimental systems—acid oligo(A) and oligo (An·Un) dimers—to exhibit the underlying stability parameters. We present a fitting procedure to extract values of the heats and entropies of the separated components when the required single‐strand data is unreliable or not available. The theory leads to length dependent heats and entropies for short single strands in a natural way, and permits a more accurate assessment of the contribution of partially bonded states in thermal transitions than has previously been possible.
Phase separation in the beta‐coil transition of poly‐S‐carboxyethyl‐L‐cysteine
Authors: Maeda Hiroshi , Ikeda Shoichi 
Published: December 2004

AbstractThe visible phase separation encountered in aqeuous system involving the β‐coil transition is investigated on poly‐S‐carboxyethyl‐L‐cysteine at a constant ionic strength of 0.2 molal. Solubility of the polymer decreases as the average charge density or pH is decreased, indicating that short‐range interactions favor the phase separation. The titration curve of the gel phase (i.e., of the pure β‐structure) is obtained by using the solubility data. Circular dichroism of the solution phase in equilibrium with the gel shows that the β‐structure is present in the solution phase. To isolate the two phases, centrifugal force is applied and it is demonstrated that the polymers in the two phases are in true equilibrium with each other. The effect of total concentration on the solubility of polymer and the degree of neutralization in each phase is interpreted in terms of the poly‐dispersity of the sample.
Optical and other properties of a hydrocarbon‐soluble polypeptide, poly‐γ‐(n‐dodecyl)‐L‐glutamate
Authors: Smith Jerry C. , Woody Robert W. 
Published: December 2004

AbstractThe polypeptide poly‐γ‐(n‐dodecyl)‐L‐glutamate (PDLG) is soluble in hydrocarbon solvents such as hexane, cyclohexane, and dodecane. The CD spectra of PLDG in these solvents are reported here. These spectra are typical α‐helix spectra and show none of the wavelength shifts and magnitude changes displayed by partially helical proteins in membrane preparations. This observation rules out the possibility that the membrane protein CD spectra result from solvent effects. The PDLG helix is stable in dodecane up to at least 70 °C. However, it is easily disrupted by trifluoroacetic acid, with the helix–coil transition centered at 3% TFA in hexane. Viscosity measurements of PDLG in dry dichloroacetic acid exhibit polyelectrolyte effects which can be suppressed by addition of several percent water.
Optical characterization of orientation of collagen
Authors: Chang E. P. , Chien James C. W. 
Published: December 2004

AbstractThe optical properties of reconstituted collagen were characterized in the frame‐work of a two‐phase model. The total birefringence is assumed to be the sum of form birefringence ΔF, of amorphous birefringence Δa, and of crystalline birefringence Δc. The contribution of ΔF has been determined as a function of strain. The intrinsic values of Δc and Δa were calculated to be 0.24 ± 0.06 and 0.055 ± 0.018, respectively. In the undeformed state, the observed birefringence is almost entirely due to the distortion of the electric field of the light at the phase boundary. Whereas there is a slight increase of form birefringence with increasing strain, the total birefringence shows much larger increments. The latter is attributable to orientation of the rodlike superstructures of the tropocollagen molecules.
Helix–coil transition and conformational studies of protamine–DNA complexes
Authors: Yu Sharon S. , Li Hsueh Jei 
Published: December 2004

AbstractProtamine–DNA complexes prepared by the method of direct and slow mixing in 2.5 × 10−4M EDTA, pH 8.0, have been studied by thermal denaturation and circular dichroism. The complexes show biphasic melting with Tm at about 50 °C corresponding to the melting of free DNA regions and Tm′ at about 92 °C corresponding to the melting of protamine‐bound regions. In protamine‐bound regions there are 1.38 amino acid residues per nucleotide, indicating a nearly completely charge neutralization. Tm is increased but Tm′ is not when the ionic strength of the buffer is raised. This also supports a full charge neutralization in protamine‐bound regions. The circular dichroism of the complexes can be decomposed into two components, Δε0 of free DNA regions in B‐form conformation and Δεb of protamine‐bound regions in a characteristic conformation neither that of B‐ nor C‐form but somewhere between them.
Electric birefringence of native DNA in an alternating field
Authors: Miller Stephen J. , Wetmur James G. 
Published: December 2004

AbstractThe relaxation of the birefringence of native DNA in solution was investigated in a pulsed sine‐wave electric field. Relaxation times were calculated from the degree of damping of the birefringence signal and were studied as a function of the strength and frequency of the applied field, the molecular weight of the DNA, and the viscosity and ionic strength of the solvent. Relaxation times decrease with increasing field strength. For high‐molecular weight DNA (>106 daltons), the relaxation times decreased with frequency and increased less than linearly with viscosity. For low‐molecular‐weight DNA (<6 × 105 daltons), the relaxation times were independent of frequency, increased linearly with viscosity, and varied with the 1.65 ± 0.1 power of the molecular weight. The average birefringence of high‐molecular‐weight DNA decreased with frequency in 0.001M Na2 EDTA plus NaOH, pH 7.0, but is much less frequency‐dependent if the EDTA concentration is reduced tenfold, while the average birefringence of sonicated DNA increases in both solvents with increasing frequency.
Circular dichroism studies on the polymerization of N‐carboxy α‐amino acid anhydride
Authors: Akaike Toshihiro , Makino Tetsuya , Inoue Shohei , Tsuruta Teiji 
Published: December 2004

AbstractThe D and L copolymerizations of N‐carboxy γ‐benzyl glutamate anhydride (NCA) were carried out in a homogeneous solution with various D/L ratios, initiated by either n‐butylamine or sodium methoxide, and were followed directly by circular dichroism (CD) to observe the behavior of the secondary structure of growing polymer molecules. In the n‐butylamine system, the difference of the helical content between the righthanded and the lefthanded (Δα‐helix) gradually increased as the polymerization proceeded, while in the sodium methoxide system, the Δα‐helix had a tendency to decrease during the later stages of the polymerization. These results suggest a difference of the power of stereo‐selection of monomer antipodes by the growing chain end between these systems, the stereoselectivity by the growing chain end in the sodium methoxide system being higher than that in the n‐butylamine system.
Effect of ionic conditions on DNA melting curve parameters
Authors: Berestetskaya I. V. , Frank‐Kamenetskii M. D. , Lazurkin Yu. S. 
Published: December 2004

AbstractSystematic experimental data for the dependence of melting range width ΔT for phage T2 and calf thymus DNA's on sodium ion concentration was obtained. A mathematical description of helix‐coil transition was given for the case of DNA with a block sequence of nucleotides (such as calf thymus DNA). This description predicts an almost linear dependence of ΔT for DNA from higher organisms on the value TGC‐TAT. On the other hand, ΔT is proportional to (TGC‐TAT)1.6 for DNA's with quasi‐random sequences (such as phage T2 DNA). Experimental data fully confirmed the theoretical predictions.The dependence of TGC‐TAT on sodium ion concentration was determined. The most striking feature of this dependence is the sharp rise in TGC‐TAT in the region of low sodium ion concentration (< 3 × 10−3) up to 100°C. The dependence of TGC and of TAT on ionic strength was calculated separately. In the region of low ionic strength, these quantities show markedly different behavior.
Influence of magnesium ions on helix–coil transition of DNA determined by modified differential scanning calorimeter
Authors: Baba Yoshihiro , Kagemoto Akihiro 
Published: December 2004

AbstractThe thermal effect of magnesium ions on the helix–coil transition of DNA was studied calorimetrically by a modified differential scanning calorimeter (DSC). It was found that the transition temperature of DNA depends on both the DNA and magnesium ion concentrations. The dependence of the helix–coil transition of DNA on the mole ratio of magnesium ions to DNA(P) can be classified into two groups. When this mole ratio is less than 1, magnesium ions tend to stabilize the double‐helix DNA, so that the transition temperature increases linearly and the heat of transition increases significantly with increasing mole ratio. When the mole ratio is more than 1, magnesium ions tend to destabilize the double‐helix DNA, so that DNA precipitates when the temperature is raised above the transition temperature. In this case, both the transition temperature and the heat of transition decrease with increasing mole ratio.
Dielectric behavior of DNA—dye complex—II
Authors: Goswami D. N. , Gupta N. N. Das 
Published: December 2004

AbstractThe dielectric relaxation of native DNA and the effect of aminoacridine dyes, such as acridine orange (AO), proflavine (PF), and ethidium bromide (EB) have been investigated at different molar DNA phosphate (P) to dye (D) ratios in the frequency range 100 Hz–100 kHz. The static dielectric constant was observed to decrease with increasing binding of aminoacridines. This was interpreted as arising from the neutralization of the surface changes of the DNA molecules as a result of dye binding. At any P/D ratio the extent of charge neutralization was greatest for AO and least for the EB–DNA complex. The relaxation time (τ) for dye‐bound DNA was greater compared to that for native DNA. This increase in τ was ascribed to the increase in the length of the dye‐bound DNA. The maximum value of τ occurred at P/D = 20, 10, and 2 for AO‐, PF‐, and EB‐treated DNA, respectively. The variation of τ at various levels of binding gave a qualitative idea about the conformational changes of DNA due to its binding with the dyes.
The optical properties of alanine and proline diketopiperazines
Authors: Hooker Thomas M. , Bayley P. M. , Radding W. , Schellman John A. 
Published: December 2004

AbstractThe optical properties of the diketopiperazine chromophore of the cyclic dipeptides have been investigated as a function of molecular conformation. The rotatory strengths of L‐alanyl–L‐alanine diketopiperazine and L‐prolyl–L‐proline diketopiperazine have been calculated as a function of the angle of fold of the diketopiperazine ring. The results of these theoretical calculations have been compared with experimental circular dichroism and optical rotatory dispersion data. It is shown that the observed optical properties of these molecules can be explained only if their diketopiperazine rings are folded in opposite directions. The direction of fold is established for each molecule. In solution, the diketopiperazine ring of L‐alanyl‐L‐alanine diketopiperazine is folded in the direction opposite to that found by X‐ray diffraction analysis of crystals. It has been observed that the degree of conservatism of the π → π* couplet of L‐propyl–L‐proline diketopiperazine depends markedly upon the nature of the solvent that is used. In addition, a shoulder has been discovered in the CD spectrum of L‐alanyl–L‐alanine diketopiperazine, which may not be directly attributable to the n → π* and π → π* transitions of the peptide chromophores.
Etude par spectroscopie infrarouge de la transformation hélice–chaîne statistique des polypeptides. II. Etude de l'interaction de quelques polypeptides à chaînes latérales polaires avec l'acide trifluoracétique
Authors: Garrigou‐Lagrange P. Combelas et C. , Lascombe et. J. 
Published: December 2004

AbstractThe various polymer–acid solvation possibilities occuring in the helix–coil transition process of polypeptides with polar side chains were systematically analyzed by infrared spectroscopy. The following samples have been considered: poly‐γ‐benzyl‐L‐glutamate (PBLG), alternating poly‐γ‐benzyl‐D,L‐glutamate (PBD‐LG), and poly‐β‐benzyl‐L‐as‐partate (PBLA). The behavior of the amide A, I, II, and νCO ester absorptions of each polymer dissolved in trifluoroacetic acid–chloroform mixtures was studied in depth. The classical assumptions concerning the interaction between a polypeptide and a proton donor solvent are discussed. This interaction was previously proposed in a theoretical model of helix–coil transition.For PBLG, the spectral characteristics of the cooperative transition are evidenced by the amide bands. These bands also show main chain–acid hydrogen bonding
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Quantitative analysis of phenomenon (I) was performed in order to localize the “binding sites” of the polymer. In agreement with the theory, only the complexation of peptide units belonging to random coil and terminal helical regions were observed. However, in contrast to the theory in which the association constants KCO and KNH of these residues are generally kept equal, the present results have shown that the main binding site is the carbonyl group (KNH ≃ 0 or « KCO).The behavior of the polar side chains of these polypeptides were analyzed during the transition. Similarly to the peptide backbone, they bind the acid by hydrogen bonding
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Furthermore, this association is more important when the side chains are localized in the coiled regions than in the helical ones. This result suggests, by analogy with the main chain behavior, that the helix–coil transition theory should take into account two more association constants for polar side chains, namely k1 for the helical regions and k2 > k1 for the coiled ones.
Polytonic studies of reconstituted collagen fibers
Authors: Balmer R. T. , Soto R. J. 
Published: December 2004

AbstractThe tensile force‐contraction characteristics of cross‐linked reconstituted collagen fibers have been studied for 30 different water‐soluble reagents. The data were obtained via a “polytonic” loading technique, which was neither isometric nor isotonic. Certain data were found to fit a master curve, which did not depend strongly on the denaturant. For many denaturants the contractile force appeared to be a maximum at a denaturant concentration corresponding to all the solvent being consumed in denaturant hydration. Also, the maximum contractile force appeared to vary in the same manner as does the hydration number of the individual cations and anions in the solution (i.e., H > Li > Na > K, and I > Br > Cl > F). Several denaturants were found to be as effective as the well‐known LiBr and KSCN in contracting the collagen.
The elastic properties of elastin
Authors: Hoeve C. A. J. , Flory P. J. 
Published: December 2004

AbstractThe thermoelastic properties of elastin immersed in water or in aqueous solutions of alcohols closely resemble those of typical polymers in the rubber elastic state. The evolution of heat much in excess of the work performed on elastin when it is stretched while immersed in water at ca. 25°C is attributable to the exothermic heat of dilution by water absorbed into the polymer during elongation. The negative sign of the temperature coefficient of swelling is confirmatory of this explanation. A network of random chains within the elastin fibers, like that in a typical rubber, is clearly indicated. The elastic properties of elastin are not explicable in terms of a two‐phase model consisting of discrete globules of compact elastin molecules fused one to another by cross‐linkages, with diluent (water) filling the interstices.
Dispersion effect on turbidimetric size measurement
Authors: Cancellieri A. , Frontali C. , Gratton E. 
Published: December 2004

AbstractIf dispersion effects are not taken into account, the dimensions of particles in suspension estimated from spectrophotometric data (slope of the log OD versus log λ plot) are too low. By measuring dispersion curves for the medium and for the suspension, a consistent estimate of the size of latex particles of different diameter is obtained from the OD data.
Binding by derivatives of polyethylenimine: Effects of charge and structure of small molecules
Authors: Johnson Timothy W. , Klotz Irving M. 
Published: December 2004

AbstractApolar derivatives of polyethylenimine in aqueous solution have been shown previously to bind organic anions very strongly. These studies have been extended to other charged and noncharged small molecules, as well as to derivatives of polyethyl‐enimine with much reduced positive charge. From these investigations the effects of charge and of structure of the small molecules can be assessed.
Thermodynamic aspects of the gelatinization and swelling of crosslinked starch
Authors: Hollinger G. , Kuniak L. , Marchessault R. H. , Marchessault R. H. 
Published: December 2004

AbstractSamples of epichlorohydrin crosslinked potato starch were prepared by using a high ratio of starch to water and alkali concentration below the gelatinization level. This yielded crosslinked samples that were partially crystalline, and where the number of crosslinks could be varied between 1 and 20 crosslinks per 100 anhydroglucose units. The degree of swelling varied regularly with degree of crosslinking, and the molecular weight between crosslinks Mc as derived from swelling data in a good swelling agent compared favorably with Mc derived from chemical analysis.From the heat of gelatinization of the crosslinked starches, as observed in a differential scanning calorimeter, for gelatinization in glycerol, water, and dimethylsulfoxide, a model for the gel state of the crosslinked starch is proposed. It is concluded that the entropy of melting is the determining factor in establishing the temperature of gelatinization.