bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for electrically induced partial strand separation of DNA
Authors: Pollak M. , Glick H. A. 
Published: May 2005

AbstractWe measured electrically induced changes of some optical properties of DNA solutions. These were the absorption coefficient and the reduced dichroism. The electric fields were applied in the form of 50–300‐μsec‐long pulses of varying field strength, up to 20 kV/cm. Changes of the optical properties were studied during the pulse. Solutions of varying DNA and salt concentrations were used. The qualitative predictions expected from the theory of electrically induced partial denaturation of the DNA were all observed. These are: (1) a decrease of the reduced dichroism at high fields; (2) a concurrent increase in the absorption coefficient; (3) a critical field above which effect (1) and (2) begin to occur; (4) a decrease of the magnitude of the above effects with increasing salt concentration; (5) a return to the status quo ante after short pulses.
The effect of ions on the enzymatic properties of beef‐liver glutamate dehydrogenase
Authors: Blauer G. , Sund H. 
Published: May 2005

AbstractThe effect of various salts on the enzymatic activity of beef‐liver glutamate dehydrogenase, on the binary enzyme‐reduced coenzyme (NADH or NADPH) comples, as well as on the ternary complex with glutamate was investigated in aqueous solution (0.067M phosphate buffer, pH 7.6). Binding studies in the analytical ultracentrifuge and circular dichroism measurements indicated dissociation of the coenzyme from the enzyme‐coenzyme complex by the action of various salts. The efficiency of this change was largely dependent on the type of anion present and generally followed the series: acetate < Br− < I− < SCN−. Acetate ions and guanidinium thiocyanate showed exceptional behaviour in some cases, while K+ and Na+ gave similar results. The reversibility of the ion effects on the enzymatic activity was demonstrated by dilution tests. Upon addition of salts, the inhibitory effect of GTP was slightly changed in most cases, while the activating effects of ADP and L‐leucine were practically abolished and with ADP, the halides caused an additional inhibition. Assuming an equilibrium involving dissociation of the enzyme‐coenzyme complex by the action of salts, an exponent of 1.3 for NaBr and of 2.0 for KSCN was calculated for the respective concentrations. The apparent equilibrium constants were evaluated to be about 20 times greater for KSCN than for NaBr.
The organization and repair of DNA in the mammalian chromosome. II. A gradient‐shape‐induced speed dependence affecting DNAs larger than T4 DNA
Authors: Lange Christopher S. , Martin Patricia , Ferguson Pamm , Resnick Michael A. 
Published: May 2005

AbstractThe addition of a lytic layer to a preformed linear sucrose gradient induces a temporary (up to half a day) initial gradient of considerable steepness which retards the sedimentation of large (>T4) DNAs. Centrifugation at sufficiently slow angular velocities permits the temporary initial gradient to disappear and therefore the sedimentation distance increases, yielding a rotor speed dependent effect on sedimentation distance. Gradients which are free of this effect are described and shown to permit mouse leukemia cell DNA to sediment independently of rotor speed (5–30 krpm).
Correlation between percentage guanine‐cytosine content and melting temperature of deoxyribonucleic acid
Authors: Tong B. Y. , Leung M. L. C. 
Published: May 2005

AbstractAn explicit relation between the percentage (G + C)‐content XGC, and the melting temperature (Tm) of a natural DNA, is derived froma a statistical mechanics calculation with due consideration given to the base pair bonding and stacking interactions. The well‐known Marmur‐Doty empirical formula, linearly relating these two quantities, can now be understood in terms of the fundamental processes. We also propose a simpler experimental procedure for the determination of XGC. It is similar to the melting temperature method, but we take only one reading at a prescribed temperature of any natural DNA in addition to the two normalization readings. It should be more sensitive for DNAs having XGC ranging from 35 to 65%.
Application of modified ising model to the helix‐coil transition of DNA molecules
Authors: Leung M. , Choo F. C. , Tong B. Y. 
Published: May 2005

AbstractEquilibrium properties of heterogeneous DNA near the melting temperature Tm are investigated using the grand partition function. The present approach gives exact and analytical solutions. The algebraic expressions enhance a more thorough understanding of the correlation among many observed equilibrium phenomena. The following quantities have been examined: melting temperature Tm, transition width W, partial melting curves θAT and θGC, mean length of a helical segment h, and correlation length γ.
Deamination of protein lysyl ε‐amino groups by peroxidase in vitro
Authors: Stahmann M. A. , Spencer A. K. 
Published: May 2005

AbstractPeroxidase, catechol, and hydrogen peroxide were shown to react with proteins, causing a decrease in lysine detectable after acid hydrolysis. The loss of lysine did not occur in the presence of benzenesulfinic acid which suggested that the quinones formed by peroxidase had oxidized some lysyl residues to lysyl aldehyde that formed a cyclic ninhydrin negative Shiff's base. When peroxidase treated protein was oxidized with performic acid prior to hydrolysis a new ninhydrin positive compound was found, which was shown by cochromatography and mass spectroscopy to be α‐aminoadipic acid. The α‐aminoadipic acid recovered accounted for (20–40)% of the lysine lost.
Conformational changes induced in ionized poly(L‐arginine) and poly(L‐histidine) by sodium dodecyl sulfate
Authors: McCord Robert W. , Blakeney Ernest W. , Mattice Wayne L. 
Published: May 2005

AbstractCircular dichroism spectra have been obtained for cationic poly(L‐arginine) and poly(L‐histidine) in aqueous solutions containing varying amounts of sodium dodecyl sulfate. The detergent induces a disorder‐order transition in both polypeptides. In each case the transition is cooperative and occurs when the ratio of detergent to amino acid residue is near unity. The ordered structure formed by poly(L‐arginine) is readily identifiable as an α helix. Poly(L‐histidine) appears to form a β structure in which the 211‐nm electronic absorption band of the imidazole group exhibits significant rotatory strength.
Synthesis and carbon‐13 nuclear magnetic resonance spectra of Cyclo(D‐leucyl‐L‐leucine) and Cyclo(L‐leucyl‐L‐leucine)
Authors: Exner Mary M. , Kostelnik Robert J. 
Published: May 2005

AbstractCyclo(D‐Leu‐L‐Leu) and cyclo(L‐Leu‐L‐Leu) were synthesized, and their carbon‐13 nmr spectra at 65 MHz were examined in dimethylsulfoxide and trifluoroacetic acid solutions. The chemical shift data are consistent with a boat or “twisted” boat conformation of the diketopiperazine ring in both solvents. There was no indication of protonation of the cyclic dipeptides by trifluoroacetic acid. Attempts at polymerizing the cyclic dipeptides were unsuccessful.
Electrical double layer, zeta potential, and electrophoretic charge of double‐stranded DNA
Authors: Schellman John A. , Stigter Dirk 
Published: May 2005

AbstractThe principal aim of this work is the proper interpretation of electrophoresis as an important tool for determining the immediate ionic environment of polyelectrolyte molecules like DNA. We also explore the relation with other experiments. We define an electrostatic model of double‐stranded DNA in monovalent salt solutions. The electrical double layer is divided in an inner Stern layer, inside the surface of hydrodynamic shear of DNA, and a Gouy‐Chapman type diffuse ionic atmosphere with cylindrical symmetry outside the shear surface. We discuss the assumptions made in applying to DNA the charge‐potential relation and the electrical free‐energy expression of the charged cylinder with a Gouy double layer. The conclusion is that reliable free‐energy data, better than 1kT per phosphate group, require a detailed model of the Stern layer. On the other hand, the Gouy model of a charged cylinder should be fairly good for the interpretation of the electrophoretic mobility of DNA. We introduce several modifications of the linear electrophoresis theory of the cylinder (Henry‐Gorin), related to the averaging over the orientations of DNA in the external electrical field, the relaxation effect, the nonlinear charge‐potential relation, and to geometrical aspects of the DNA model. Applied to published mobility data the modified theory yields roughly the same ζ potentials as before, but DNA charges which are about twice as high as derived earlier from the linear Henry‐Gorin theory. The charge calculation is quite sensitive to the assumed geometrical model of DNA. Our electrophoresis results are somewhat higher than the charges derived from Donnan equilibria of DNA in monovalent salt solutions measured by Strauss et al. The required self‐consistency of electrophoretic charge and ζ potential of DNA as a function of the salt concentration is treated on the basis of adsorption of counterions to the DNA phosphate groups (site binding). It is predicted that at low ionic strength the electrophoretic charge of DNA should be independent of the salt concentration.
Poly(L‐lysyl‐L‐alanyl‐α‐L‐glutamic acid)
Authors: Goren H. Joseph , Fletcher T. , Epand R. M. 
Published: May 2005

AbstractPoly(Lys(Cbz)‐Ala‐Glu(OBzl)) was prepared by the self‐condensation of Lys(Cbz)‐Ala‐Glu(OBzl)‐ONSu in dimethylformamide. After deprotection of the side chains, the product was subjected to Sephadex G‐50 chromatography. The molecular weight of unfractionated and fractionated poly(Lys‐Ala‐Glu) was calculated from a calibrated Sephadex G‐50 column, spectrophotometrically from Dnp‐(Lys‐Ala‐Glu), equilibrium centrifugation, and viscosity measurements. Approximately 21% of the unfractionated material was polymeric with the remaining 79% being cyclic and monomeric material. Treatment of polymer hydrolysate with L‐amino acid and D‐amino acid oxidase indicated poly(Lys‐Ala‐Glu) to be optically pure. The apparent pKa's of the two ionizable groups were 4.1 and 9.7.
15N nmr spectroscopy. I. Polysarcosine and related sequence polypeptides
Authors: Kricheldorf Hans R. , Hull William E. , Formacek Viktor 
Published: May 2005

AbstractThe natural abundance 15N nmr spectra of linear polysarcosine (DP = 35) has been recorded in Me2SO and H2O solution. Because of cis/trans isomerization at the peptide bond, a broad signal with several splittings was observed. These splittings appear to reflect the influence of three peptide bonds on a single N atom. The 15N signals from the sequence polypeptides (β‐Ala‐Sar‐Gly)n and (β‐Ala‐Sar‐D,L‐Ala)n also show a cis/trans splitting, as well as chemical shifts which are dependent on the peptide sequence. The tertiary nitrogen of the sarcosyl residue has a T1 relaxation time which is longer than the T1 for secondary nitrogens of the other amino acids. The nuclear Overhauser effect is also discussed.
d‐CpCpGpG and d‐GpGpCpC self‐complementary duplexes: Nmr studies of the helix‐coil transition
Authors: Patel Dinshaw J. 
Published: May 2005

AbstractWe have monitored the helix‐coil transition of the self‐complementary d‐CpCpGpG and d‐GpGpCpC sequences (20mM strand concentration) at the base pairs, sugar rings, and backbone phosphates by 360‐MHz proton and 145.7‐MHz phosphorus nmr spectroscopy in 0.1M phosphate solution between 5 and 95°C. The guanine 1‐imino Watson‐Crick hydrogen‐bonded protons, characteristic of the duplex state, are observed below 10°C, with solvent exchange occurring by transient opening of the tetranucleotide duplexes. The cytosine 4‐amino Watson‐Crick hydrogen‐bonded protons resonate 1.5 ppm downfield from the exposed protons at the same position in the tetranucleotide duplexes, with slow exchange indicative of restricted rotation about the C‐N bond below 15°C. The guanine 2‐amino exchangeable protons in the tetranucleotide sequence exhibit very broad resonances at low temperatures and narrow average resonances above 20°C, corresponding to intermediate and fast rotation about the C‐N bond, respectively. Solvent exchange is slower at the amino protons compared to the imino protons since the latter broaden out above 10°C. The well‐resolved nonexchangeable base proton chemical shifts exhibit helix‐coil transition midpoints between 37 and 42°C. The transition midpoints and the temperature dependence of the chemical shifts at low temperatures were utilized to differentiate between resonances located at the terminal and internal base pairs while the H‐5 and H‐6 doublets of individual cytosines were related by spin decoupling studies. For each tetranucleotide duplex, the cytosine H‐5 resonances exhibit the largest chemical shift change associated with the helix‐coil transition, a result predicted from calculations based on nearest‐neighbor atomic diamagnetic anisotropy and ring current contributions for a B‐DNA duplex. There is reasonable agreement between experimental and calculated chemical shift changes for the helix‐coil transition at the internal base pairs but the experimental shifts exceed the calculated values at the terminal base pairs due to end‐to‐end aggregation at low temperatures. Since the guanine H‐8 resonances of the CpCpGpG and d‐CpCpGpG sequences exhibit upfield shifts of 0.6–0.8 and <0.1 ppm, respectively, on duplex formation, these RNA and DNA tetranucleotides with the same sequence must adopt different base‐pair overlap geometries. The large chemical shift changes associated with duplex formation at the sugar H‐1′ triplets are not detected at the other sugar protons and emphasize the contribution of the attached base at the 1′ position. The coupling sum between the H‐1′ and the H‐2′ and H‐2″ protons equals 15–17 Hz at all four sugar rings for the d‐CpCpGpG and d‐GpGpCpC duplexes (25°C), consistent with a C‐3′ exo sugar ring pucker for the deoxytetranucleotides in solution. The temperature dependent phosphate chemical shifts monitor changes in the ω,ω′ angles about the O‐P backbone bonds, in contrast to the base‐pair proton chemical shifts, which monitor stacking interactions.
Kinetics of complex formation between fluorescein mercuric acetate and DNA
Authors: Takeuchi Shintaro , Maeda Akio 
Published: May 2005

AbstractThe kinetics of complex formation between fluorescein mercuric acetate and heat‐denatured DNA were studied by measuring the fluorescence quenching of this reagent. This quenching process involved no immeasurably rapid phase and it was shown that this reaction follows simple second‐order kinetics. The rate constant at 25°C was estimated to be 2.9 × 104M−1 sec−1 for calf‐thymus DNA (42% G + C) and 1.1 × 104M−1 sec−1 for Micrococcus lysodeikticus DNA (72% G + C). Activation parameters for this reaction were calculated from the temperature dependence of the reaction rate, and the activation entropy was found to be highly negative (−27.5 cal/mol deg for calf‐thymus DNA and −25.5 cal/mol deg for M. lysodeikticus DNA). The binding of fluorescein mercuric acetate to native DNA, which requires the opening of the double‐helical structure, was also followed by measuring the absorbance change of this reagent. There was a lag phase in this binding process, and the enthalpy change for the opening step corresponded roughly to that for the opening of one base pair. These findings are discussed in relation to the results of a similar study with formaldehyde.
Circular dichroism of the nucleic acid monomers
Authors: Sprecher Cindy A. , Johnson W. Curtis 
Published: May 2005

AbstractCircular dichroism spectra of the nucleic acid monomers have been measured in aqueous solution and extended into the vacuum ultraviolet region to about 166 nm. Measurements were made on ribo and deoxyribo derivatives of adenine, guanine, hypoxanthine, cytosine, thymine, and uracil derivatives both with and without the 5′‐phosphate (with the exception of ribosyl thymine 5′‐phosphate). Absorption spectra of the deoxyribonucleotides measured to about 175 nm are also presented. The results demonstrate that both the circular dichroism and absorption spectra observed below 200 nm are no more complicated than the spectra normally recorded above 200 nm. In most cases, the circular dichroism spectra of the various derivatives of a given base are similar, indicating that the conformations are similar. On the other hand, the differences among the circular dichroism spectra of the various derivatives of a given base are sufficient to identify a particular derivative. The average circular dichroism for the deoxyribonucleotides is compared with the circular dichroism of native E. coli DNA. The comparison reveals that the circular dichroism of DNA below 200 nm is due principally to the interaction between the bases rather than the intrinsic circular dichroism of the monomers. The monomer transitions are discussed in relationship to the absorption and circular dichroism spectra presented.
Molecular arrangement of DNA in bacteriophage T4
Authors: Basu Samarendra 
Published: May 2005

AbstractThe degree of preferred orientation and the coiling of the deoxyribonucleic acid within phage T4 was studied by two independent techniques, namely, polarization of fluorescence and uv linear dichroism. A correlation between the two kinds of data was obtained, which indicated that a significant proportion (about 30%) of total phage DNA is aligned preferentially along the long axis of phage heads. Analyses of the data suggest that all of the phage DNA cannot be in a highly supercoiled helical configuration. A few models of the DNA arrangement in T4 have been discussed in which linear sidewise packings of DNA would be predominant and may explain the observed longitudinal orientation of intraphage DNA.
Helix‐coil stability constants for the naturally occuring amino acids in water. XIV. Methionine parameters from random poly(hydroxypropylglutamine,L‐Methionine)
Authors: Hill D. J. T. , Cardinaux F. , Scheraga H. A. 
Published: May 2005

AbstractWater‐soluble, random copolymers containing L‐methionine and N5‐(3‐hydroxypropyl)‐L‐glutamine have been prepared, fractionated, and characterized. The thermally induced helix‐coil transitions of these copolymers in water have been investigated, and it has been found that incorporation of L‐methionine increases the helix content of the polymers at all temperatures in the range of 0–60°C. The Zimm‐Bragg parameters σ and s for the helix‐coil transition in poly(L‐methionine) in water were deduced from an analysis of the melting curves of the copolymers using the methods described in earlier papers.
A new procedure for refining force constants in normal coordinate calculations on large molecules
Authors: Van Zandt L. L. , Lu K.‐C. , Prohofsky E. W. 
Published: May 2005

AbstractWe develop a force‐constant refinement procedure which we believe capable of being used in problems of large molecules and biopolymers. The procedure is based on a Green‐function expression which relates changes in frequency to changes in force constants. The method does not require that assignments be made before refinment (although they may be). An expansion of this expression gives rise to a set of linear algebraic equations for the force‐constant corrections, rather than an equation involving residuals to minimize. The resulting calculations are considerably simpler. This approximate is iterated to find the final refined force‐constants. We discuss several methods of improving the convergence of the procedure which take into account the experimental information which may be available. Of particular interest is a scheme to select the force constants to be refined by imposing a criterion for selecting those which will fit the experimental data with the smallest changes of the force constants from their expected values. We discuss some limitations which occur for all methods of refinement applied to large molecules.
Sequential polypeptides by matrix‐controlled thermal polymerization. Synthesis and racemization studies
Authors: Sakarellos‐Daitsiotis Maria , Gilon Chaim , Sakarellos Constantinos , Goodman Murray 
Published: May 2005

AbstractA new method for the synthesis of sequential polypeptides is described. The approach consists of the thermal condensation in vacuo of the trifluoroacetate salts of tripeptide pentachlorophenyl esters deposited on a micron‐size celite matrix. The synthesis and polymerization of the trifluoroacetate salts of L‐valy‐L‐valyl‐L‐alanine pentachlorophenyl ester, glycyl‐L‐valyl‐L‐alanine pentachlorophenyl ester, and L‐valyl‐L‐alanylglycine pentachlorophenyl ester are described. High‐molecular‐weight polymers are obtained rapidly in high yield by this method. Comparison of the extents of racemization in the last two polymers constitutes a general approach for assessing racemization during the synthesis of sequential polypeptides since both yield the same polymer, but only the C‐terminal alanine may recemize in the former case.
n‐Mer binding on a one‐dimensional lattice of two‐state m‐site cells: Heavy meromyosin on regulated actin as an example
Authors: Tsuchiya Takashi , Hill Terrell L. 
Published: May 2005

AbstractHeavy meromyosin binding to F‐actin saturated with tropomyosin is studied theoretically. The problem is formulated as a special case of n‐mer adsorption to a one‐dimensional Ising lattice which is divided into m‐site‐long blocks.
Vacuum‐ultraviolet circular dichroism of chondroitins and their complexes with poly(L‐arginine)
Authors: Stipanovic Arthur J. , Stevens E. S. 
Published: May 2005

AbstractThe vacuum‐ultraviolet circular dichroism (VUCD) of chondroitin and chontroitin‐6‐sulfate has been measured to 160 nm for films and to 170 nm for D2O solutions. The pD‐dependent dichroic behavior of these glycosaminoglycans in D2O is similar above 200 nm and is in agreement with previous studies. Near 190 nm, the CD band sign is also dependent on pD. VUCD spectra were recorded for films and solutions of poly(L‐arginine). In trifluoroethanol the polypeptide is α‐helical, while in D2O it exists as a random coil. The well‐characterized coil–helix transition of poly(L‐arginine) during complexation with chondroitin‐6‐sulfate was observed by VUCD, including the previously inaccessible entire π → π* band. By construction of difference spectra it was also possible to monitor the VUCD of the polysaccharide component during complexation.
Nmr study of poly(aspartic acid). I. α‐ and β‐Peptide bonds in poly(aspartic acid) prepared by thermal polycondensation
Authors: Pivcová H. , Saudek V. , Drobník J. , Vlasák J. 
Published: May 2005

AbstractThe structure of poly(aspartic acid) prepared by thermal polycondensation has been studied by means of nmr spectroscopy. The analysis of the 13C‐nmr spectra of the polymer at various pH values and comparison with the spectrum of poly(α‐L‐aspartic acid) revealed that the polymer contained aspartic acid linked in α‐ and β‐peptide bonds. The mole fraction of the β‐peptide bonds has been found to be 0.8 ± 0.1. The significance of the results for the evolutionary theory of S. W. Fox is mentioned.
Nmr study of poly(aspartic acid). II. α‐ and β‐Peptide bonds in poly(aspartic acid) prepared by common methods
Authors: Saudek V. , Pivcová H. , Drobník J. 
Published: May 2005

AbstractThe nature of peptide bonds in poly(aspartic acid) prepared by debenzylation of poly(β‐benzyl‐L‐aspartate) under various conditions has been studied by means of nmr spectroscopy. It was established that the majority of the polymers prepared, as well as the commercially obtained polymer, contained aspartic acid linked in both α‐ and β‐peptide bonds. The purest polymer, having practically undetectable amounts of β‐bond, was prepared by debenzylation by HBr in trifluoroacetic acid. It was established that the β‐bonds are formed via succinimides.