bluuebunny/crossref_metadata_2025 huggingface dataset:
Helix–random chain transitions of polyamino acids in organic acid–salt solutions
Authors: Franzen James S. , Bobik Caroline , Harry John B.
Published: December 2004

Polyamino acids which are soluble and helical in acetic acid and dichloroacetic acid (DCA) have been observed to undergo a helix to random chain transition upon the addition of lithium salts of strong acids. The transition can be reversed by diluting the salt. Apparently only lithium cations are able to bring about the polycarbobenzoxy‐L‐lysine (PCBL) transition in acetic acid, whereas the anions display a varying degree of effectiveness; ClO4− > Br− > TSA− > Cl− > NO3−. The lithium salts of carboxylate anions such as OAc− and TFA− do not cause polymer unwinding in acetic acid. Neither do the acids, TSA, HCl, TFA, or DCA induce the transformation in acetic acid. Poly‐L‐alanine (PLA) in DCA unfolds as LiBr is added, but does not unfold in the presence of 0.5M (CH3)4NBr, 0.25M CsBr, or 0.32M HCl. These results are explained on the basis of a direct interaction of the lithium salt with the polymer amide groups to form an ion‐pair complex. The extent to which the union of the ion pair can dissociate from the complex in the low dielectric constant, environment determines the degree of unfolding of the polymer. The anion dissociation equilibrium presumably therefore would lie in the same order as given above. Acids such as HCl and TSA are considered to substantially protonate and ion‐pair with the polymer, but do not readily dissociate the anion partner from the complex, and therefore do not produce an unstable positively charged helical structure.
Study of helix–coil transition of DNA by dielectric constant measurement
Authors: Takashima Shiro
Published: December 2004

The thermal helix–coil transition of DNA was studied by means of dielectric constant measurements. The dielectric dispersion of native helical DNA is characterized by a large dielectric increment and a large relaxation time, whereas that of denatured coil DNA is characterized by a small dielectric increment and a small relaxation time. The dielectric dispersion of partially denatured DNA is of particular interest. At the intermediate stage of the helix–coil transition, dispersion curves which are different from either that of helix DNA or that of coil DNA appear. This is particularly pronounced for large DNA. This indicates the presence of an intermediate form of DNA. Flow birefringence measurements were carried out simultaneously. The negative birefringence of helical DNA diminishes as the helix–coil transition proceeds. However, the extinction angle remains constant, as long as it can be measured. These results indicate the absence of intermediate forms during the helix–coil transition. The discrepancy between dielectric and birefringence measurements can be resolved by assuming that the intermediate forms are not birefringent. The size distribution of native DNA and of the indicated intermediate form of DNA was studied. It is found that a logarithmic normal distribution function explains the distribution of size of DNA reasonably well.
Polymerization of γ‐benzyl‐L‐glutamate N‐carboxy‐ anhydride: Effects of conditions of polymer precipitation on the molecular weight distribution
Authors: Peggion Evaristo , Scoffone Ernesto , Cosani Alessandro , Portolan Antonio
Published: December 2004

Poly‐γ‐berizyl‐L‐glutamate prepared by polymerization of γ‐benzyl‐L‐glutamate NCA in dimethylformamide (DMF) with the use of diisopropylamine as the initiator was precipitated from the polymerization mixture under different conditions. A portion of the almost completely polymerized solution was treated with an excess of isopropylamine and then precipitated into diethyl ether (sample A). The remaining portion of the polymerization mixture was concentrated in a rotating evaporator, stored at room temperature for a few days, and then diluted with DMF and precipitated into diethyl ether (sample B). The molecular weight distributions of the two polymer samples were determined by the chromatographic procedure of Baker and Williams. The molecular weight of sample B is roughly three times that of sample A. However both samples have the “most probable” distribution of molecular weight. The results are interpreted according to Bamford's polymerization mechanism.
Reconstruction of protein and nucleic acid sequences. V. Computer‐simulated tests of various tactics for reconstructing the sequences of transfer ribonucleic acids
Authors: Merril Carl R. , Shapiro Marvin B. , Bradley Dan F. , Mosimann James E. , Vinton Jay E.
Published: December 2004

One hundred hypothetical polynucleotides of varying chain length and composition and of random sequence were generated and their chemical degradation simulated by a computer. Included in the study were 20 hypothetical polymers with the composition and chain length of a transfer RNA. A second computer program attempted to reconstruct the sequences from the nucleotide composition and the simulated fragments produced. Approximately 700 reconstructions were attempted from various sets of fragments generated from the 100 polymers. The dependence of the probability of reconstructing the original sequences on the methods of producing and isolating the fragments was studied.
Topological considerations in protein structure. I. Disulfide linkage
Authors: Kato Ikunoshin , Narita Kozo , Fuke Ichita
Published: December 2004

The patterns of disulfide bridges in proteins were considered by using the concept of topological information content. It was proposed that the difference between topological informal ion content in the half‐cystine residues of the native state and of the fully reduced form of a protein is related to the problems of the renaturation of the fully reduced and denatured protein. Specifically, when there is no difference between the topological information contents of the two states, the reduced protein is able to recover its native conformation. The concept reported in the present paper is consistent without exception with reported experimental results.
Sedimentation coefficient of T‐even bacteriophage DNA
Authors: Rosenbloom J. , Cox E. C.
Published: December 2004

The sedimentation coefficient of T2 phage DNA has been studied by zone centrifugation in sector‐shaped preparative centrifuge tubes over a concentration range of 0.02–2.0 μg./ml. DNA. These results have been compared to a similar study in the analytical centrifuge of T4 DNA over the range of 0.50–5.75 μg./ml. DNA. A value for the sedimentation coefficient of 60.7 ± 1.8 S. was obtained by the first method and a value of 61.3 ± 1.5 S. by the second.
Solution properties of synthetic polypeptides. I. Light scattering and osmometry of poly‐γ‐benzyl‐L‐glutamate in helicogenic solvents
Authors: Fujita Hiroshi , Teramoto Akio , Okita Koichi , Yamashita Tsuneko , Ikeda Shoichi
Published: December 2004

Light‐scattering measurements were performed for a number of poly‐γ‐benzyl‐L‐glutamate (PBLG) samples in dimethylformamide (DMF) and in chloroform‐formamide (C‐F) at 25°C. Osmotic pressure data for some of these polypeptide samples in DMF at 37°C. were also determined. The scattering radii 〈S2〉1/2 in the two solvents were roughly proportional to the sample's weight‐average molecular weight Mw. The lengths per monomeric residue h, calculated from the measured 〈S2〉1/2 and Mw with the assumption of a rigid rod of uniform density, were about 1.2 A. in DMF and about 1.5 A. in C‐F. The measured values for the Mw/Mn ratio indicated that the samples used were quite polydisperse in molecular weight. If this effect is taken into account, the above values for h must be lowered drastically. In fact, application of Holtzer's procedure, which is capable of yielding h free of polydispersity effects, gave 0.85 A. for h in DMF and 1.16 A. for h in C‐F. Since, according to the recent conclusion established by Parry and Elliott, the correct conformation of the PBLG molecule in helicogenic solvents must be the α‐helix for which h is 1.5 A., these results imply that the overall shape of the PBLG helix cannot be a rigid rod, in contradiction to the earlier conclusion of Doty et al.
Denaturation and renaturation of DNA. I. Equilibrium statistics of copolymeric DNA
Authors: Montroll Elliott W. , Goel Narendra S.
Published: December 2004

The one‐dimensional Ising model, with nearest neighbor correlation only, suitably modified, is used to explain the observed linear dependence of melting temperature of copolymeric DNA with GC content. Transition curves are plotted for regular, random, and Markoff distribution of base pairs for various values of a correlation parameter U between nearest neighbor bonds. Exact analytic formulas are given for fraction of bonds intact at a particular temperature for various regular distributions for all U and approximate ones for random and Markoff distributions for small U. A scheme is indicated for further improvement. The model, in principle, makes it possible to estimate the statistical distribution of base pairs from the detailed shape of the transition curve.
Interaction of aminoacridines with deoxyribonucleic acid: Viscosity of the complexes
Authors: Drummond D. S. , Pritchard N. J. , Simpson‐Gildemeister V. F. W. , Peacocke A. R.
Published: December 2004

The intrinsic, viscosities at zero shear rate of defined complexes of proflavine, 9‐aminoacridine, and 9‐amino‐l,2,3,4‐tetrahydroaeridine with calf thymus DNA have been determined at, various ionic strengths by means of rotating cylinder viscometers. By controlled adjustment, of the composition of the mixtures, the amount of bound acridine (r moles/g.‐atom DNA phosphorus) was maintained constant at different dilutions. The intrinsic viscosities of the complexes increased with r up to r values (ca. 0.16–0.20) corresponding to the end of the process of strong binding of the acridinium cations. However, complex formation between the acridines and thermally denatured DNA caused either a marked decrease in viscosity (at the low ionic strengths of 0.0015 and 0.005) or no change at all (ionic strength 0.1). These results are discussed in the light of presently available hydrodynamic theories relating the intrinsic, viscosity of DNA to its molecular extension.
Properties of thyroglobulin. XII. Comparison of the configurational states of reduced and unreduced thyroglobulin
Authors: Edelhoch H. , Steiner R. F.
Published: December 2004

The relaxation time of thyroglobulin has been determined in water at. neutral pH, in concentrated urea and guanidine solutions, at alkaline pH, both before and after reduction with β‐mercaptoethanol. The structure of thyroglobulin in concentrated urea solutions is markedly affected by the pH, Time‐dependent changes occur in thyroglobulin in concentrated urea or guanidine solutions which arc observable by polarization of fluorescence but not by optical rotation or viscosity. The reduction of the disulfide crosslinks of thyroglobulin in urea at high pH or in guanidine produces linear polypeptide chains with few if any permanent contacts between segments.
Mesure de la dispersion diélectrique en très basse fréquence de solutions de DNA
Authors: Hanss Maxime
Published: December 2004

Based on the four electrodes technique, an apparatus is described which measures the Very Low Frequency (VLF) conductivity of ionic solutions, all electrode effects being completely eliminated. It is thus possible to measure the conductivity frequency dependence between 0.8 and 500 cps, with a relative error of 10−4. Applying this method to DNA solutions, one always finds a conductivity dispersion in the VLF range, which disappears when the biopolymer is heat‐denatured. The relaxation time is different from one solution to another, but is always greater than 10 msee. approximately, sometimes even greater than 0.1 sec., the upper limit which one can estimate with our apparatus. The different, explanations of the DNA very low frequency polarization, assuming that its relaxation is connected with the rotational diffusion of the biopolymer long axis, is discussed.
Optical rotatory dispersion of E. coli ribosomes and their constituents
Authors: Sarkar P. K. , Yang J. T. , Doty Paul
Published: December 2004

Investigations have been made on the optical rotatory dispersion properties of E. coli ribosomes and their constituent RNA and proteins. The results indicate that (1) no conformational changes are involved in the formation of a 70S particle from the 50S and 308 subunits, (2) the E. coli ribosomal proteins are similar to most globular proteins with little α‐helix content, and (3) the conformation of RNA and proteins inside the ribosome is very similar to that in the free state.
Wechselstrompolarographische kriterien der nucleinsäuredenaturierung
Authors: Berg H. , Bär H. , Gollmick F. A.
Published: December 2004

The electrochemical possibilities for investigation of nucleic acids with high molecular weight are restricted to the determination of the adsorption behavior. According to our experience the alternating current polarography (Breyer‐polarography) is mainly appropriate for the characterization of changes in the secondary structure of DNA. The Breyer‐polarogram shows the alternating current of the dropping electrode in dependence on their potential which varied from 0–2 v. negative against the normal calomel electrode (NCE). By addition of native DNA to the supporting electrolyte (buffer solution) the current drops down in the range of adsorption between 0 and 1 v. At 1.16 v. against NCE the desorption takes place together with the formation of a rounded desorption peak. The investigation was carried out in phosphate buffer solution 0.1m with 0.075m NaCl or in a phosphate buffer 0.18m with 0.03m NaCl. In the pH range above pH 8 NaOH was added to realize the higher pH values. A calf thymus DNA sample having a mean molecular weight of about 18 million was used. The concentration of DNA was 5 × 10−3−1 × 10−1 wt.‐%. The polarographic measurements were performed with an a.c./d.c.‐polarograph “GWP 564” from Akademiewerkstätten für Forschungsbedarf der Deutschen Akademie der Wissenschaften zu Berlin (DAW). The denaturation of the double helix causes a sharp desorption peak at negative potentials of the alternating current polarogram. This new criterion for the helix‐coil transition is due to formation of unpaired bases. These nearly free bases undergo a specific adsorption and the desorption takes place within a narrow potential range. Nevertheless, at present time an electron transfer to particular bases cannot be excluded at special conditions. The increase of the sharp peak permits to estimate: (a) the melting curve of the double helix in agreement with spectroscopic measurements; (b) the photolysis of the double helix; (c) the strand separation in acid and alkaline solution. In the alkaline range the sharp peak increases and reaches its maximum at pH > 12. In the acid range, however, no sharp peak is observed and the rounded desorption peak decreases. Therefore, the best way of following the conformation changes is to measure the current difference between the curves of the solutions with and without DNA at electrocapillary‐zero‐potential. On the classical d.c.‐polarogram one can measure small current steps only, which may be caused mainly by capacity changes. Moreover, the scission of the molecule by ultrasonic action can be followed. In this case the rounded peak of DNA increases but the sharp peak does not appear. Similar alternating current polarograms are obtained with poly‐A in the native state, because helical and unordered regions coexist in the same molecule. The very rapid indication of these structure changes allows one to carry out kinetic measurements at a fixed potential with this method.
Structure of branched poly‐α‐amino acids in dimethylformamide. I. Light scattering
Authors: Eliezer N. , Silberberg A.
Published: December 2004

Light scattering of multichain poly‐α‐amino acids was studied in dimethylformamide (DMF). The polymers consisted of a backbone of poly‐L‐lysine of degree of polymerization n with side chains of benzyl L‐glutamate and benzyl L‐aspartate of degree of polymerization, m, on each ε‐amino group. The backbone length n is known and m is obtained by amino acid analysis. The results on a series of such materials confirm this structure and show that the molecules are dissolved in highly compacted conformations. It was found that DMF is a poor solvent for these polymers. In the case of the higher molecular weight polymers, the solutions initially were not molecularly disperse. The aggregates were resistant to dilution in the experimental range. Mild heat treatment, however, disaggregated the solutions irreversibly, and the light‐scattering data indicated that a structural rearrangement of the molecules had occurred.
Dynamic viscoelastic properties of solutions of shear‐degraded deoxyribonucleic acid
Authors: Meyer H. H. , Pfeiffer William F. , Ferry John D.
Published: December 2004

Calf thymus and salmon sperm deoxyribouncleie acid were degraded by high‐shear stirring to molecular weights M in the range of 1.3–3.2 × 106 and purified by chromatography on methylated bovine serum albumin. Dynamic viscoelastic properties of the fragmented products, in aqueous glycerol solutions in the concentration range of c = 0.003–0.01 g./ml., were investigated with the apparatus of Birnboim and Ferry. At values of the product cM higher than 4 × 103, the frequency dependence of the components of the complex shear modulus, G′ and G″, displayed a plateau region in which G′ > G″ – ων1ηS, similar to that observed in concentrated solutions of coiling polymers where it is attributed to an entanglement network (ω is radian frequency, ν1 volume fraction of solvent, and η8, solvent viscosity). The width of this plateau region on the logarithmic frequency scale is given by Δ = 3.8 (log cM – 3.56). At lower values of cM, the frequency dependence is intermediate between those predicted by the theory of Zimm for flexible coiled macromolecules and by the theory of Kirkwood and Auer for rods. Fitting to the Zimm theory gives highly discrepant values for molecular weights, while fitting the low‐frequency end of the dispersion to the Kirkwood‐Auer theory gives reasonable agreement for both molecular weight and rotary diffusion coefficient. It is concluded that the helical fragments appear as nearly rigid rods in their behavior at very low frequencies, but at higher frequencies reveal substantial bending flexibility.
Eleclrophoresis of adsorbed DNA
Authors: Chattoraj D. K. , Chowrashi P. , Chakravarti K.
Published: December 2004

The electrophoresis mobilities of native calf thymus DNA adsorbed on the charged solid particles were measured by a micro‐electrophoretic method as functions of pII, ionic strength, and DNA concentration. The mobility data confirm the adsorption of DNA both on the positively charged alumina and negatively charged resin particles at wide range of pH and ionic strength. The mobility data also indicate significant DNA adsorption by negatively charged glass in the acidic range of pH. The electrophoretic mobilities of DNA adsorbed on different substrate particles under identical conditions do not differ widely, indicating the major role of the adsorbed DNA rather than the covered substrate in controlling the charge behavior of the particle. The mobilities of the adsorbed DNA at salt pH are of a comparable order of magnitude to those for the dissolved DNA in solution. The mobility of the adsorbed heat‐denatured and alkali‐denatured DNA is lower than that of the native adsorbed DNA under identical conditions of pH and ionic strength.
Studies of polypeptide structure by fluorescence techniques. III. Interaction between dye and macromolecule in fluorescent conjugates
Authors: Gill Thomas J. , McLaughlin E. M. , Omenn Gilbert S.
Published: December 2004

The effects of pH on the polarization of fluorescence of dyes dissolved in media of high viscosity or conjugated to polypeptides that undergo no structural transitions indicate that DNS is useful for studying pH‐dependent molecular transition over the range pH 2.5–14, whereas fluorescein is useful only over the range pH 6–8. Heating and cooling in aqueous solutions cause no change in the polarization of fluorescein or of DNS; therefore, the dyes themselves do not introduce artifacts into heating studies of the dye conjugates. The interaction between fluorescein or DNS and the molecule to which it is conjugated varies and thus may affect the measurements made with the conjugates: the rotational relaxation times of polylysine, of a copolymer of glutamic acid and lysine, and of lysozyme are approximately twice as long when measured with DNS‐conjugates as when measured with fluorescein‐conjugates. The explanation for this observation is postulated to lie in the tighter binding between fluorescein and the molecule to which it is conjugated, presumably around the point of its covalent attachment, which makes it a better indicator of the behavior of the rotational kinetic unit of the polypeptide chain. The stronger binding of fluorescein is inferred from two lines of evidence: (1) the fluorescent intensity and ultraviolet spectra of a fluorescein–polylysine conjugate are less susceptible to changes in solvent than those of the DNS conjugate, and (2) the net charge of the polypeptide affects the ionization of fluorescein much less than it affects the ionization of DNS. Additional evidence from previous studies corroborates this conclusion. Thus, it is important to establish the relationship between the fluorescent dye and the molecule to which it is conjugated before using the fluorescence data to calculate rotational relaxation times and other molecular parameters.
Synthèse et structure de la poly‐O‐carbobenzoxy L‐ tyrosine et de copolymères de O‐carbobenzoxy L‐tyrosine et de glutamate de benzyle ou d'aspartate de benzyle
Authors: Vollmer Jean‐Pierre , Spach Gérard
Published: December 2004

The optical rotatory dispersion of copolymers of O‐carbobenzoxy‐L‐tyrosine and benzyl L (or D)‐glutamate as well as benzyl L‐aspartate, dissolved in nonpolar solvent, has been studied. Moffitt's equation permits the determination of b0 coefficients whose variation, with varying composition in amino acid residues, suggests that the molecules of poly‐O‐carbobenzoxy‐L‐tyrosine have a helical structure similar to that of poly‐(benzyl L‐glutamate). Results obtained from infrared spectroscopy and x‐ray diffraction show that the copolymers possess a helical conformation in the solid state, even when they are very rich in carbobenzoxy‐L‐tyrosine residues. The value of the b0, coefficient for poly‐O‐carbobenzoxy‐L‐tyrosine may be explained by a regular stacking of the chromophore groups around the helical backbone. The ordering of the molecules of this polymer in a purely helical structure seems favored by the insertion of a small number of foreign residues in the polypeptide chain.
Activity coefficients of counterions in solutions of diethylaminoethyl dextran hydrochloride
Authors: Gubenšek F. , Lapanje S.
Published: December 2004

Activity coefficients of counterions in solutions of diethylaminoethyl dextran hydrochloride have been determined. It has been observed that they increase with decreasing concentration of the polyelectrolyte. The experimental values have been compared with those calculated using Oosawa's theory of activity coefficients. The calculated values are higher than those observed, which suggests that the rodlike model on which Oosawa's theory is based is inadequate for the present case. Activity coefficients of counterions of some solutions containing NaCl and KC1, respectively, have also been determined. It has been found that the additivity rule for activity of counterions applies for these solutions.
NMR and optical activity observations on the helix–coil transition in poly(γ‐benzyl L‐glutamate) solutions
Authors: Liu Kang‐Jen , Lignowski J. S. , Ullman Robert
Published: December 2004

The helix–coil transition of poly(γ‐benzyl L‐glutamate) was studied by comparing proton magnetic relaxation behavior with optical activity studies. The transition temperature as determined by magnetic relaxation was lower than that obtained by optical activity. The concentration dependence of the transition was also studied. The relationship of these experiments with previous NMR studies and also with calorimetric investigation of the transition is developed.
Origin of branches in native dextrans
Authors: Ebert K. H. , Brosche M.
Published: December 2004

According to the proposed mechanism for the enzymatic formation of dextran, branches of different length are formed in a reaction between a so‐called acceptor dextran molecule and an active reaction complex; propagation of the dextran chain occurs by an insertion‐type polymer growth. To investigate this branching reaction, radioactive labeled acceptor dextran of relatively low molecular weight was added to a dextran synthesizing system and the native high molecular weight dextran separated by a fractionation method. From the specific radioactivity of the isolated native dextran, and assuming a molecular weight of 2.5 × 105, the average number of acceptor molecules incorporated into native dextran is calculated to be about unity, as predicted by the proposed mechanism. Analogous results have been obtained in the reaction of two different dextran sucrases from Leuconostoc mesenteroides B512F and B1307, respectively.
Rotatory dispersion of the β‐form of polypeptides
Authors: Volkenstein M. V. , Zubkov V. A.
Published: December 2004

The rotatory dispersion of the β‐form of polypeptides is considered. The parameter b0 of the Moffit‐Yang equation is calculated quantum mechanically. The results obtained b0 = −30, agrees with experiment which gives b0 near zero for the β‐form.
Spectrophotometric titration studies on poly (uridylic acid)
Authors: Simpkins H. , Richards E. G.
Published: December 2004

In order to provide preliminary data for the interpretation of the spectrophotometric titration properties of RNA, the spectral changes accompanying the ionization of poly‐(uridylic acid) have been determined, as have the ionization constants as a function of salt concentration and the enthalpies and entropies of ionization. The spectral propertics and ionization constants of poly (uridylic acid) have been compared with those of 2′(3′) Uridine monophosphate and of uridine; significant, differences have been established. The results obtained are consistent with the hypothesis that uracil residues in poly U are stacked only in concentrated salt solutions.
Experimental thermodynamics of the helix–random coil transition. I. Influence of polymer concentration and solvent composition in the PBG–DCA–EDC system
Authors: Ackermann Theodor , Neumann Eberhard
Published: December 2004

The course of the reversible helix formation of poly(γ‐benzyl L‐glutamate) (PBG) dissolved in a mixture of dichloroacetic acid (DCA) and 1,2‐dichloroethane (EDC) was followed by measuring the heat capacity and the optical rotation of the system through the transition region. The results of these measurements indicate that the transition enthalpy ΔH the transition temperature Tc, and the Zimm‐Bragg parameter σ depend considerably on the PBG concentration as well as on the composition of the solvent. For the standard state of infinite dilution, however, a linear extrapolation of the measured ΔH if values results in a standard value ΔH° = 950 cal./mole, independent of the solvent composition. The results of the calorimetric measurements are discussed in relationship to changes in optical rotation. Some peculiarities in the measured thermodynamic and optical properties in solutions with relatively high content of dichloroacetic acid are reported.
Variation in the intensity of scattered light by solutions of DNA subjected to an electric field
Authors: Scheludko A. , Stoylov S.
Published: December 2004

Preliminary experiments have been carried out which measure the variation in the intensity of the light scattered by DNA solutions under the influence of an electric field. Data have been collected on the length of DNA molecules, their electric polarizability, and their dispersion behavior.
Topography of nucleic acid helices in solutions. II. Structure of the double‐stranded rA–rU, rI–rC, acid rA, and the triple‐stranded rA–rU2 and rA–rI2 helices
Authors: Gabbay Edmonxd J.
Published: December 2004

Information concerning the structures of rA–rU, rA–rU2 rI–rC, rA–rI2, and acid rA helices in solutions is reported. Through the use of diquaternary ammonium salts of the general structure, \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm R}_1 {\rm R}_2 {\rm R}_3 \mathop {\rm N}\limits^ + ({\rm CH}_2 )n\mathop {\rm N}\limits^ + {\rm R}_1 {\rm R}_2 {\rm R}_3 \cdot 2{\rm Br}^ - $\end{document} (I), it is shown that (1) the distances between adjacent negatively charged oxygen atoms on the helix increases in the following order rA–rI2 < rI–rC < rA–rU ⩽ rA–rU2; (2) the density of the helices increases in the order. rA–rI2 < rA–rU < rA–rU2 < rI–rC; (3) there is a large hydrophobia site in rA–rI2 and possibly also in rA–rU, rA–rU2, and rI–rC helices; (4) the results of the interactions between the salts of type I and the helices may be formulated in semi‐quantitative terms by the use of two parameters, α, and β which are shown to be related to the charge separation and the density of the helices, respectively; (5) the studies in solutions compare favorably with the x‐ray studies on the fibers; and (6) the acid rA helix differs significantly from the other helices by the fact that the electrostatic interstrand interactions between the negatively charged oxygen atom of a phosphate group and the positively charged 10‐amino group of adenine contribute significantly to the stabilization of the helix, and thus it is found that the presence of the salts, I, leads to a significant destabilization of the acid rA helix.
Conformational analysis of poly‐N‐methyl‐L‐alanine
Authors: Liquori A. M. , De Santis P.
Published: December 2004

Sterically allowed forms of the poly‐N‐methyl‐L‐alanine chain were found by calculation of conformational energies as a function of the rotation angles of its chain bonds. The lowest energy form seems to be a right‐handed, approximately threefold helix.
X‐Ray diffraction of oriented amylose fibers. II. Structure of V amyloses
Authors: Zobel H. F. , French A. D. , Hinkle M. E.
Published: December 2004

Oriented amylose fibers in the V form were prepared and subjected to x‐ray analysis. Unit cells and the probable space group of P212121 were determined for the V anhydrous and V hydrate forms of amylose; the analysis confirms previous predictions of these structures based on x‐ray powder patterns. Chain folding in V amyloses is discussed in view of crystallographic evidence and folding experiments conducted with space‐filling models. Reported also is evidence for amylose helices having diameters intermediate between 13.0 and 13.7 A.
Complexing and denaturation of DNA by methylmereuric hydroxide. II. Ultracentrifugation studies
Authors: Gruenwedel Dieter W. , Davidson Norman
Published: December 2004

When increasing concentrations of methylmercuric hydroxide are added to a Cs2SO4 solution of native DNA, the buoyant density of DNA is unaltered until a critical concentration is reached above which there is a cooperative transition to denatured DNA which now binds so much CH3HgOH that it becomes very dense and nonbuoyant. As increasing concentrations of methylmercuric hydroxide are added to a Cs2So4 solution of denatured DNA, the buoyant density gradually increases, indicating a gradual increase in the amount of methylmercury cation bound. The denatured DNA methylmercury complex becomes nonbuoyant at the same concentration of methylmercuric hydroxide as does the native DNA. These results support our previous interpretation that CH3HgOH reacts with the imino NH bonds of thymine and guanine in nucleic acids. The reaction occurs more or less independently at the different binding sites for denatured DNA, but it occurs cooperatively with simultaneous denaturation for native DNA. The nature of the transition of denatured DNA to the nonbuoyant state is not known, but it is probably due to an abrupt decrease in the degree of hydration of the DNA when its density and hydrophobic character are sufficiently increased by the binding of the methylmercury cation. Direct measurements of the amount of methylmercury bound by DNA, as observed by preparative ultracentrifugation, confirm approximately the buoyant density results as to the amount of methylmercury bound. The possibility of using methylmercuric hydroxide as a reagent for the separation of complementary strands, depending on then thymine of their thymine plus guanine content, is discussed.
Statistical mechanical studies of polypeptides. I. Theory of the helix–coil transition including right and left‐handed helical states
Authors: Scott Roy A.
Published: December 2004

The Lifson‐Roig and Zimm‐Bragg theories of the helix–coil transition in polypeptides are generalized to include both right‐ and left‐handed α‐helical states. The partition functions for these more general theories are formulated in terms of the parameters u, vR, VL, WR, and wL for the generalized Lifson‐Roig theory and σR, σL, sR, and sL for the generalized Zimm‐Bragg theory. Matrix equations are derived for calculating such average molecular properties as the fraction of the amino acid residues hydrogen bonded into right‐ and left‐handed α‐helices, the average number of right‐ and left‐handed helical sequences per molecule, the number‐average length (in residues) of the right‐ and left‐handed helical sequences, and the degree of solvent binding to the peptide NH and CO groups. These equations are shown to be conveniently adaptable to machine methods of calculation, thus avoiding the difficulty of solving an eigenvalue problem where the secular equation is of a high order. A discussion is given of the various energetic and entropic effects which determine the screw sense and stability of helices and of the extent to which it is valid to interpret experimental data by adjustment of the parameters of these statistical mechanical theories which include in their formulation only near‐neighbor interactions between residues.
Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH
Authors: Record M. Thomas
Published: December 2004

An approximate analytical expression for the electrostatic free energy of a polynucleo‐tide in any of its possible ordered or random conformations is derived by integration of the screened‐Coulomb potential energy function over all charge pairs in the structure. The electrostatic free energy of any form is found to be a linear function of the logarithm of the monovalent counterion concentration, in the range of low salt concentrations. Hence the electrostatic free energy difference between ordered and disordered forms in a polynucleotide structural transition is a linear function of the logarithm of the monovalent counterion concentration. A free energy balance applied to a two‐state model for the transition then yields a linear dependence of the transition temperature Tm upon the logarithm of the counterion concentration. Calculation of the quantity dTm/d log M, where M is the monovalent counterion concentration, shows it to be a characteristic constant for a given transition, with a magnitude and sign proportional to the charge density difference between the ordered and disordered forms. Use of any one of several alternate, simple assumptions yields predicted dTm/d log M values in good agreement with experimental data for various polynucleotide transitions.
Numerical solutions of the Lamm equation. IV. Rotor slowing experiments
Authors: Billick Irwin H. , Dishon Menachem , Weiss George H. , Yphantis David A.
Published: December 2004

This paper presents the results of a numerical solution of the Lamm equation for roton slowing specified by ω2 = ω02 exp {– λτ}, for parameters relevant to equilibrium experiments. It. is shown that in the two‐component system it is theoretically possible to deduce s/D from measurements of the difference of concentration across the. cell with rotor slowing, provided that the time at which the difference reaches a maximum is known.
Relaxation kinetics of denaturation of DNA
Authors: Goel Narendra S.
Published: December 2004

The one‐dimensional Ising model, with nearest‐neighbor correlations only, used earlier in equilibrium studies of melting of DNA is extended to study the relaxation kinetics of copolymeric synthetic DNA near the melting temperature. An exponential kinetics, in agreement with the observations, has been found.
Effect of carcinogens and related compounds on the semiconductive properties of protein
Authors: Snart Ronald S.
Published: December 2004

The d.c. electrical conductivity of solid gels of bovine plasma albumin, under high vacuum, shows a semiconductive behavior which is sensitive to small amounts of complexed carcinogens and related compounds. The effect of these compounds on the electrical properties of the protein provides evidence of an interaction which may be related to the carcinogenic activity.
Electrophoresis of absorbed RNA
Authors: Chowrashi P. K. , Chattoraj D. K. , Chakravarti K.
Published: December 2004

The electrophoretic mobilities of adsorbed yeast ribonucleic acid have been measured as functions of pH, ionic strength, and biopolymer concentration and the results so obtained have been critically compared with those for adsorbed DNA. Like DNA, ribonucleic acid has also been found to reverse the positive charge of alumina owing to its adsorption on the solid‐liquid interface. The mobilities of adsorbed RNA have been found to be less than those of adsorbed DNA under identical conditions. The observed mobilities of adsorbed heat‐ and alkali‐denatured RNA are significantly less than those of adsorbed native RNA at a given pH and ionic strength of the medium. The electrophoretic mobilities as observed also show the evidence of RNA adsorption on the negatively charged surface of Dowex‐50 resin, but practically no adsorption of RNA on the negatively charged glass surface has been predicted.
Flow birefringence of T2 bacteriophage DNA
Authors: Harrington Rodney E.
Published: December 2004

The streaming birefringence and extinction angles of DNA from T2 bacteriophage in neutral aqueous buffers have been determined over a range of concentrations from 5 to 44 μg./ml. and of velocity gradients from 5 to 50 sec.−1. Although the extinction angles are relatively small even at the lowest velocity gradients and concentrations studied, a lower limit estimate of the limiting extinction angle to shear rate ratio can be made, and this value is interpreted in terms of available dynamical theory. The statistical segment length has been estimated from the birefringence data as ∼ 1100 A. This figure is in satisfactory agreement with the results of independent calculations by others.
Calculation of melting curves for DNA
Authors: Crothers Donald M.
Published: December 2004

A method is reported for calculating the melting curve of a DNA molecule of random base sequence, including in the formalism the dependence of the free energy of base pair formation on the size of a denatured section. Some explicit results are shown for a “typical” base sequence, in particular the probability of helix formation at individual base pairs in several different regions of the molecule and the amount of melting from the end of the chain. Particular attention is drawn to the variation of local melting behavior from one region of the molecule to another. It is found that sections rich in AT melt at relatively low temperatures with a fairly broad transition curve, whereas regions rich in GC pairs melt at higher temperatures (as expected) with a very abrupt, local transition curve. To account qualitatively for the results one may divide melting into two kinds of processes: (a) the nucleation and growth of denatured regions, and (b) the merging together of two denatured sections at the expense of the intervening helix. The first of these processes dominates in the first stages of melting, and leads to rather broad local melting curves, whereas the second process predominates in the later stages, and occurs, in a particular part of the molecule, over a very narrow temperature range. It is estimated that the average length of a helix plus adjacent coil section at the midpoint of the transition is approximately 600 base pairs. Since transition curves which measure the local melting behavior reflect local compositions fluctuations, these curves contain information about the broad outlines of base sequence in the molecule. Some suggestions are made concerning experiments by which this potential information source could be exploited. In particular, it is pointed out that one might hope to map AT or GC rich regions at particular genetic loci in a biologically active DNA molecule. Values of the relevant parameters found earlier for the transition of homopolymers produce melting curves for a DNA of random base sequence which are in good agreement with the experimental transition curve for T2 phage DNA. Hence the present theoretical picture of the melting of polynucleotides is at least internally self‐consistent.
Optical anisotropy of synthetic polynucleotides. I. Flow birefringence and π‐electron polarizabilily of bases
Authors: Takashima Shiro
Published: December 2004

Birefringence of poly‐A, poly‐U, and double‐stranded poly‐AU are investigated experimentally as well as theoretically. Single‐stranded poly‐A, at low ionic strength, exhibits a strong negative birefringence indicating that, adenine molecules are stacked regularly with their planes along the transverse direction. On the addition of Mg or Mn ions, the birefringence decreases markedly. Poly‐U has no noticeable birefringence indicating that poly‐U has a contracted configuration in solution. On mixing poly‐A and poly‐U with 10–3M MgCl2, the birefringence increases markedly, but the change in the chain configuration seems less pronounced. The polarizability of adenine and uracyl are ejaculated using the simple Ifïückel scheme. The calculation shows that the π‐electron polarizability normal to the base plane is zero. Therefore, the negative birefringence is probably due to the lack of π‐electron polarizability in the direction normal to the base plane and accordingly no π‐electron polarizability along the major helix axis. Conversely, the negative birefringence is an indiaction of base stacking.
Determination of stability of the DNA double helix in an aqueous medium
Authors: Privalov P. L. , Ptitsyn O. B. , Birshtein T. M.
Published: December 2004

The possibility of determining the free energy of stabilization ΔG0 of native DNA structure with the help of calorimetric data on heats ΔH of transition from the native to denaturated state is considered. Results of microcalorimetric measurements of heats of denaturation of T2 phage DNA at, different values of pH and ionic strength of solution are given. Values of free energy of stabilization of the DNA native structure ΔG0 under various conditions have been obtained. It is shown that under conditions close to physiological ΔG0 approaches 1200 cal/mole per base pair.
Poly(L‐leucyl‐L‐ornithyl‐L‐leucine) and its Guanidization Product: Synthesis and Antibacterial Activity
Authors: Fridkin M. , Frenkel A. , Ariely S.
Published: December 2004

The synthesis of poly(L‐leucyl‐L‐ornithyl‐L‐leucine) and of poly(L‐leucyl‐L‐arginyl‐L‐leucine) is reported. The antibacterial action of the two copolymers was checked by growth inhibition experiments on Staphylococcus aureus. The activity was found to be identical with that of a disordered 1:1 copolymer of L‐ornithine and L‐leucine. Conversion of 75% of the ornithine residues to arginine had no effect on the antibacterial activity.
Physicochemical properties of N4 virus solutions. I. Viscosity–temperature behavior
Authors: Rialdi Giovanni , Profumo Pietro , Ciferri Alberto
Published: December 2004

The viscosity–temperature behavior of N4 virus solution was investigated by using a Zimm type viscometer. The role of ionic strength (LiBr) and pH in the viscosity–temperature behavior was determined. Supporting measurements of the sedimentation coefficient, infectivity, and optical density are presented. The viscosity–temperature behavior generally includes a region of low viscosity, characteristic of the intact virus, followed, upon increasing temperature, by a rather abrupt increase of viscosity which corresponds to the ejection of native DNA from the protein shell, presumably through a suitable opening in the capside. The viscosity remains constant upon further increase of temperature until a second abrupt increase is observed which is shown to correspond to the degradation of the empty protein shell (ghost). Finally, at a still higher temperature, denaturation of DNA occurs. This sequence of events can be altered by changes in pH and ionic strength. Increasing LiBr concentration reduces the temperature of ghost degradation and raises the temperature of DNA ejection and DNA de naturation. It is suggested that polyelectrolyte effects play a controlling role in the ejection of native DNA and that the conformation of the latter within the protein shell is stabilized by a decrease of the electrostatic free energy due to the swamping effect of the co‐ions.
Extraction, separation and labeling with 14C‐glucose of hela cell polyglucose, RNA and DNA and comparison of the molecular weights and buoyant densities of polyglucose from poliovirus‐infected and noninfected cultures
Authors: Graves I. L.
Published: December 2004

The aqueous phase of phenol extracts of HeLa cells contains polyglucose (CHO)n, RNA, and DNA. These macromolecules were precipitated together and removed from 50% (v/v) ethanol solutions with a stirring rod. The viscous precipitate had the classical white appearance of DNA, but contained an average of 439, 670, and 220 μg (from 3 × 107 cells) of (CHO)n, RNA, and DNA, respectively. The (CHO)n was separated from the RNA, either by CsCl density gradient centrifugation or by precipitating the RNA with trichloroacetic acid (TCA). Both methods of separation resulted in preparations of (CHO)n with similar specific activities (radioactive counts/μg min). However, electron micrographs showed that the (CHO)n separated by using TCA had a greater variation in particle size when compared with (CHO)n separated by CsCl centrifugation. With the CsCl methods, the number‐average molecular weights, as determined by electron microscope particle‐counting, and the buoyant densities of (CHO)n whose synthesis was stimulated by poliovirus infection and (CHO)n from noninfected cultures, were found to be similar. When the (CHO)n was extracted from HeLa cells with TCA, rather than phenol, the yield was 1.68‐fold greater and its specific activity was an average of twice that of the (CHO)n extracted with phenol. The time at which cells were pulse‐labeled with 14C‐glucose, after reducing the glucose in the culture medium to 0.01 of normal, was found to be important, in that the specific activity of the (CHO)n increased 23.4‐fold over a 4‐hr period and the amount extracted decreased 8.2‐fold. The increase in the specific activities of RNA and DNA was not as large as that of the (CHO)n and the amounts extracted were not significantly changed. The sedimentation coefficients of RNA and (CHO)n which were separated from each other with TCA were 6.4 and 116 S, respectively, whereas, without separation, two peaks were seen, with values of 25.4 and 31.4 S. Chloride ions reduce the sensitivity of the Burton test for DNA. However, the Burton reagent will detect (CHO)n even in the presence of DNA if the assay mixture is heated. Chloride ions increase the sensitivity of the Burton reagent to detect melizitose and, at concentrations above l.5M, synthetic‐ polyglucose by increasing the absorption of the colored (CHO)n reaction product(s).