bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cooperative nonenzymic base recognition—a study of interaction of oligoguanylic acid with poly C
Authors: Podder S. K. 
Published: December 2004

AbstractThe interaction between poly C and (Gp)nG(n = 1,2) in dilute solution was investigated spectrophotometrically in 0.1M phosphate buffer pH 7.2 under conditions unfavorable for the formation of self‐associated complexes of oligoguanylic acids. Two isosbestic points were observed when poly C was titrated gradually with GpGpG, one at 232–233 mμ(in the range of 0–33% poly C) and one around 238 mμ (in the range of 50–100% poly C). The melting temperature (Tm) of the 1:1 poly C: (Gp)nG complexes (n = 1,2) of varying concentration were determined. The equilibrium properties of the 1:1 complexes can be described by two interaction parameters, namely, (i) cooperative stacking interaction between the first nearest neighbor of the adsorbed oligomer, and (ii) intrinsic association constant of the adsorbed oligomer with its polymeric site, since the cooperative helix–coil transition particularly in the smaller oligonucleotide can be described by an “all or none” model. Based on such a model the enthalpy of stacking inteaction‐dependent Tm values yielded directly the sum of the enthalpy of stacking interaction and of basepairing (which is dependent on the chain length of the oligomer) and the value of S, the stability constant of a G–C pair within a helix. The enthalpy of formation of G–C pair is then calculated as −6.3 kcal/base pair either from the chain length dependent enthalpy term or from the temperature coefficient of S values. From the S value and the association constant of 1:1 GpGpGpC:GpCpCpC complex, other thermodynamic parameters such as nucleation parameter (β) and free energy of stacking interaction can be obtained.
Induced cotton effects of tRNA–acridine orange complex and tRNA conformation
Authors: Ito Takashi , Zama Mitsuo , Amagasa Jumpei 
Published: December 2004

AbstractCircular dichroism spectra of acridine orange bound to E. coli tRNA were studied at varying tRNA phosphate‐to‐dye (P/D) ratios for both unfractionated and purified materials in the absence of Mg++. From the rather discrete features exhibited in the circular dichroism spectra three types of interactions were observed: (1) A high P/D ratio such as 75.2 or 49.8 indicates the interaction between the nucleotide base and dye molecule. The spectra with a large positive peak at 515 mμ are, however, quite different from that of DNA–AO complex under similar conditions. (2) With an intermediate P/D ratio (26.5 to 9.6) dye molecules bound strongly to the polynucleotide chain. (3) With low P/D ratios (≤7.5) the interaction appears to be due to the stacked dye molecules in the single‐stranded part of tRNA. The spectra of the third group have an isobestic point at 477 mμ. Below a P/D ratio of 4 the spectrum shows one positive and two negative bands which may be the characteristics of circular dichroism of stacked dyes in polynucleotide chain.Although no drastic change in the conformation of tRNA itself was detectable in the presence of Mg++ in the ultraviolet region, a dramatic change was observed in the circular dichroism of tRNA–acridine orange complex when Mg++ concentration was increased to 10−3M. It was inferred that certain conformational changes other than simple hydrogen bond formation occured in tRNA molecules at this high Mg++ concentration, so that the amount of bound dye in the stacking condition was increased through the transition.
Model connective tissue system: The effect of proteoglycans on the distribution of small non‐electrolytes and micro‐ions
Authors: Preston B. N. , McK. Snowden J. , Houghton K. T. 
Published: December 2004

AbstractDonnan equilibria between solutions of various carbohydrates polyins and Na⊕ have been measured by equilibrium dialysis. From the results, estimates have been made of the degree of Na⊕ fixation by the polyions. Comparison is made between the behavior of the complex proteoglycan macromolecules and their constituent glycosaminoglycans. Attempts to interpret these results and the Na⊕ activity in saltfree solutions on the parameter of the intercharge distance has been made. By use of studies on carboxymethylcellulose, the relative importance of the carboxyl and of the sulphate ester groups in the Na⊕ fixation is assessed. The relevance of the measurements to the previously described diffusional effects found in real and model connective tissues is discussed.
The kinetics of the renaturation of deoxyribonucleic acid denatured in the presence of copper (II) ions
Authors: Holman Lynette R. , Jordan D. O. 
Published: December 2004

AbstractDNA which has been heat denatured in the presence of Cu++ ions can be completely and rapidly renatured by increasing the ionic strength of the solution above a critical value. A kinetic study of this renaturation recation was carried out by following the associated UV absorbance change and also by following the change in free Cu++ ion concentration by means of a specific Cu++ ion activity electrode. The data obtained could be fitted to first‐order kinetics for a considerable extent of the reaction and the rate constant was found to increase with temperature and ionic strength, but to decrease markedly as the bulk viscosity of the solution was increased. At temperatures greater than 5°C the reaction rate depended on the time elapsing between denaturation and the commencement of the renaturation reaction. As there was good agreement between the rate constants obtained by following the decrease in hyperchromism and by following the increase in free Cu++ ion concentration, it is concluded that under the conditions employed, the rate of renaturation is determined by the rate of release of Cu++ ions from the denatured DNA‐Cu++ complex.
The conformation of histone f2a1 (histone IV) in solution at low inoic strength
Authors: Ziccardi Robert , Schumaker Verne 
Published: December 2004

AbstractHydrodynamic studies of histone f2a1 are performed in dilute salt solution. Protein sedimentation is shown to be dependent upon the partial specific volume and molarity of the supporting electrolyte. To compensate for the secondary chage effect, a solvent of dilute tetramethylammonium chloride, for which (1 − V̄saltρ) ≅ 0, is used. To correct for the primary charge effect in sedimentation, a special linear extrapolation to infinte dilution of the protein is employed. Measurements of intrinsic viscosity are interpreted in terms of an increase in molecular dimension with a decrease in ionic strength. The conformation of histone f2a1 in dilute salt solution is interpreted from sedimentation and viscosity data to be that of a highly charged random coil possessing 20–30% of nuclear globular structure.
Raman studies of the helix‐to‐coil transition in poly‐L‐glutamic acid and poly‐L‐ornithine
Authors: Koenig J. L. , Frushour Bruce 
Published: December 2004

AbstractThe conformational transitions in water and in the solid state of poly‐L‐glutamic acid (PGA) and poly‐L‐ornithine (PO) have been studied by Raman spectroscopy. The Raman spectra of PGA, PO, and the monomer, dimer, and trimer of PGA in aqueous solutions and solid state are presented. The Raman spectral changes of PGA and PO were followed through the helix‐to‐coil transition induced by pH, temperature, and solvent composition. A hyperchromic shift in the intensity of the amide III line accompanying the helix‐to‐coil transition was observed. This hyperchromic intensity shift occurs abruptly as a function of pH but more slowly with heat denaturation of the alpha helix indicating that the Raman spectrum is sensitive to the transition mechanism. The high‐temperature coil and the charged coil may have different conformations as evidenced by different amide III frequencies but similar intensities in these two conformations.
Sedimentation equilibrium of DNA samples heterogeneous in density
Authors: Schmid Carl W. , Hearst John E. 
Published: December 2004

AbstractThe problem of determining the molecular weight of DNA samples by sedimentation equilibrium in a buoyant‐density gradient is considered for the case of DNA samples with density heterogeneity. By determining apparent molecular weights in two or more buoyant mediums, quantitative measure of the amount of density heterogeneity can be determined. This method may be employed to determine both the true molecular weight and the extent of base composition heterogeneity.
The linear dichroism of oriented helical and superhelical polymers
Authors: Rill Randolph L. 
Published: December 2004

AbstractExpressions are derived to relate the linear dichroism of oriented helical and super‐helical polymers to the vector equation describing a transition moment in a reference frame based on the position of a single monomer unit in a simple helix and the super‐helix tilt angle β. The reduced dichroism of a perfectly oriented superhelical polymer, (Δε/ε)0, is related to the reduced dichroism of a perfectly oriented helical polymer, (Δε/ε)1, by the expression (Δε/ε)0 = ½ (Δε/ε)1(3 cos2 β − 1). Hence the linear dichroism of a helical polymer can be significantly altered by supercoiling. The application of the general expressions is illustrated by the derivation of specific equations which relate the dichroism of helical and superhelical DNA to the tilt and twist of the DNA bases, the directions of the transition moments within the base planes, and the superhelix tilt angle. Calculations of the reduced dichroism of perfectly oriented, non‐super‐helical DNA in the A and B configurations suggest that it will be difficult to distinguish between these two forms on the basis of dichroism measurements.
Poly(L‐alanine): Investigation of alpha‐helix and betal‐sheet forms by low‐temperature specific heat measurements (1.5–20°K)
Authors: Finegold Leonard , Cude Jesse L. 
Published: December 2004

AbstractFor an ideal one‐dimensional solid, the low‐temperature specific heat, C, is proportional to temperature T1, for an ideal two‐dimensional solid C is proportional to T2. We have observed such one‐ and two‐dimensional behavior in alpha‐ and beta‐poly(L‐alanine) in the temperature range 1.5–20°K (also intermixed with a three‐dimensional behavior). A specific heat anomaly has also been observed. These measurements are important in evaluating the effective elastic constants, including hydrogen bonding, of the biopolymers. They also provide essential information for vibrational theories of poly(L‐alanine), which up until now have been based on high‐energy data.
On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. V. Ionic effects on renaturation kinetics
Authors: Manning Gerald S. 
Published: December 2004

AbstractThe bimolecular rate constant k2 for the association of complementary polynucleotide strands has been observed to increase strongly with increasing ionic strength—in fact, proportional to its third or fourth power. This effect is here interpreted quantitatively by means of polyelectrolyte theory starting with the Wetmur–Davidson postulate of a pre‐equilibrium between separated strands and aligned segments close to one another but unbonded. The correct form, a power dependence of k2 on ionic strength, is predicted. Comparison of the theoretical exponent with data allows the conclusion that each of the two single‐stranded segments in the aligned but unbonded configuration consists of about 13–16 nucletides (not to be confused with the much smaller number of bonded base pairs in the nucleus), and that this number, denoted by Q, is possibly correlated either with a minimum length for duplex stability or with the persistence length of a single polynucleotide strand. It is suggested that experimental determination of the dependence of Q on (G+C)‐content may distinguish between these possibilities. It is also suggested that addition of sufficient amounts of divalent metal ions such as Mg2+, Ca2+, or Co2+ may reverse the dependence of k2 on ionic strength; under these conditions, k2 is predicted to decrease with about the first power of ionic strength. At fixed ionic strength, k2 should increase with increasing concentration of divalent metal ion, and, in fact, the published observation that the formation of poly(A)·2 poly(U) from poly(A)·poly(U) and poly(U) is second order in Mg2+ concentration is here correctly predicted from a priori molecular considerations. Finally, published association rate data for oligonucleotides are discussed in the present theoretical context.
Interaction of aminoacridines with deoxyribonucleic acid: Effects of ionic strength, denaturation, and structure
Authors: Drummond D. S. , Simpson‐Gildemeister V. F. W. , Peacocke A. R. 
Published: December 2004

AbstractThe binding curves of various aminoacridines on calf thymus DNA have been determined by a spectrophotometric method. The dominant role of electrostatic forces in the interaction has been confirmed by the effect of ionic strength. Side chain and ring substituents in the aminoacridines do not inhibit binding, since this decreases in the order: acranil > neomonacrin > atebrin > 9‐aminoacridine ∼ proflavine > 9‐amino‐1,2,3,4‐tetrahydroacridine (THA). The last named shows the effect of diminishing the flat area of the rings in the aminoacridines. The shape of the binding curves of proflavine, 9‐aminoacridine, and THA on thermally denatured DNA show that about 30–50% more binding sites are available to these cations on denatured DNA than on native DNA, but that the binding constants are the same. These observations are discussed in relation to the intercalation and other models for the interaction. It is concluded that exact and complete intercalation is not a necessary condition of strong binding and that other, less regular, models, in which the positive ring nitrogens of the acridines are close to the DNA phosphates and the acridine rings partially interact with the DNA base rings, are probably more consistent with the effect of denaturation of DNA on the binding curves which are characteristic of the interaction in solution.
Statistical mechanics of noncovalent bonds in polyamino acids. I. Hydrogen bonding of solutes in water, and the binding of water to polypeptides
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractBy using the Nemethy‐Scheraga theory of water structure, a calculation was made of the energy changes for the rupture of a DH…︁A solute–solute hydrogen bond in water. A partition function was also obtained for the binding of water and other solutes to the DH and A groups in the special case where these are the NH and CO groups of a random coil polypeptide chain. In subsequent papers of this series, these calculated quantities will be used in a statistical mechanical treatment of the helix–coil transition for polypeptides in water.
Statistical mechanics of noncovalent bonds in polyamino acids. V. Treatment of long chains by the method of sequence‐generating functions: Hydrophobic bonding in random coil, and interactions between helical segments
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractThe method of sequence‐generating functions is applied to long polypeptide chains to describe various types of hydrophobic bonding in the random coil. These results are then combined with a similar treatment of the α‐helix in order to discuss the helix–coil transition in single helices and in molecules whose helical segments interact by side‐chain hydrophobic bonding. Numerical calculations, based on the equations derived in this and preceding papers, are presented to show the relative probabilities of occurrence in the random coil of neighbor–neighbor hydrophobic bonds and pockets of hydrophobic bonding, and the relative probabilities of occurrence of the various states in a system of interacting helices. A discussion is also presented of the dependence of the helix–coil nucleation and growth parameters on solvent and side chain.
NMR study of the secondary structure of s‐RNA
Authors: McDonald C. C. , Phillips W. D. , Penswick John 
Published: December 2004

AbstractThe melting characteristics of unfractionated yeast s‐RNA in neutral aqueous solution have been examined by high‐resolution proton magnetic resonance spectroscopy. These studies indicate that the bases of s‐RNA become rotationally activated at lower temperatures than their associated ribose units. These observations, as well as the recently determined base sequence of an alanine‐specific s‐RNA, suggest that base complementarity may not be the primary determinant in the stabilization of the secondary structure of s‐RNA. In addition, evidence for exchange of C8‐protons of purine bases of s‐RNA with D2O was obtained at temperatures above 70°C.
Precision space‐filling atomic models
Authors: Koltun Walter L. 
Published: December 2004

AbstractShortly, lightweight, inexpensive, precision, space‐filling atomic models particularly suitable for constructing macromolecules of biological interest will reach the scientific community. The availability of the models, the Corey‐Pauling‐Koltun, or C‐P‐K Models, will conclude a five‐year program which has involved the cooperative efforts of Federal agencies, scientific societies, and selected scientists. This paper describes the development of the program, details the contributions of the various groups and persons who have been involved, and discusses the technical characteristics of the models.
Impact of external calcium and calcium sensors on ginsenoside Rb1 biosynthesis by Panax notoginseng cells
Authors: Yue Cai‐Jun , Zhong Jian‐Jiang 
Published: December 2004

AbstractThe effects of external calcium concentrations on biosynthesis of ginsenoside Rb1 and several calcium signal sensors were quantitatively investigated in suspension cultures of Panax notoginseng cells. It was observed that the synthesis of intracellular ginsenoside Rb1 in 3‐day incubation was dependent on the medium Ca2+ concentration (0–13 mM). At an optimal Ca2+ concentration of 8 mM, a maximal ginsenoside Rb1 content of 1.88 ± 0.03 mg g−1 dry weight was reached, which was about 60% and 25% higher than that at Ca2+ concentrations of 0 and 3 mM, respectively. Ca2+ feeding experiments confirmed the Ca2+ concentration‐dependent Rb1 biosynthesis. In order to understand the mechanism of the signal transduction from external Ca2+ to ginsenoside biosynthesis, the intracellular content of calcium and calmodulin (CaM), activities of calcium/calmodulin‐dependent NAD kinase (CCDNK) and calcium‐dependent protein kinase (CDPK), and activity of a new biosynthetic enzyme of ginsenoside Rb1, i.e., UDPG:ginsenoside Rd glucosyltransferase (UGRdGT), in the cultured cells were all analyzed. The intracellular calcium content and CCDNK activity were increased with an increase of external Ca2+ concentration within 0–13 mM. In contrast, the CaM content and activities of CDPK and UGRdGT reached their highest levels at 8 mM of initial Ca2+ concentration, which was also optimal to the ginsenoside Rb1 synthesis. A similar Ca2+ concentration‐dependency of the intracellular contents of calcium and CaM and activities of CCDNK, CDPK, and UGRdGT was confirmed in Ca2+ feeding experiments. Finally, a possible model on the effect of external calcium on ginsenoside Rb1 biosynthesis via the signal transduction pathway of CaM, CDPK, and UGRdGT is proposed. Regulation of external Ca2+ concentration is considered a useful strategy for manipulating ginsenoside Rb1 biosynthesis by P. notoginseng cells. © 2004 Wiley Periodicals, Inc.
Fermentation mixing scale‐up techniques
Authors: Oldshue J. Y. 
Published: December 2004

AbstractScale‐up of a mixing process in fermentation involves breaking the process down into individual but interrelated steps. The effect of mixing on gas‐liquid absorption, fluid shear rates, blending, and heat transfer allows each to be considered separately. A method of estimating the mixer size required in a full‐scale system from pilot studies illustrates the application of a particular technique.
Kinetics of polysaccharide B‐1459 fermentation
Authors: Moraine R. A. , Rogovin P. 
Published: December 2004

AbstractPolysaccharide gum was made by fermentation with Xanthomonas campestris NRRL B‐1459 in a medium of glucose, minerals, and distillers' solubles. The effect of distillers' solubles on growth rate can be described by the familiar saturation equation. Although a quasistoichiometric relationship was observed between nitrogen utilization and growth, total nitrogen supply was not growth limiting, nor was polymer formation growth associated. Cell growth primarily took place in the early part of the fermentation; polysaccharide biosynthesis occurred throughout the fermentation. Glucose was converted to polysaccharide at a fairly constant yield, which was 70–80% of glucose consumed, under optimum conditions. The kinetic patterns observed indicate that multistage continuous fermentation will be suitable for polysaccharide production.
Utilization of gas oil by a yeast culture
Authors: Miller Thomas L. , Johnson Marvin J. 
Published: December 2004

AbstractA mixed yeast culture (Culture 4) was grown on representative gas oil samples as well as paraffin wax. Culture 4 was found to utilize n‐paraffinic hydrocarbons almost quantitatively from most gas oil fractions; significant alteration of other hydrocarbon components was not detected. Generation times of 4.0–9.0hr. were typical during the exponential growth phase in fermentations with various gas oil fractions. Cell yields were 70–90% based on n‐paraffin utilization. The culture appeared to exhibit maximum efficiency of n‐alkane removal in the C19 to C24 range. The cells recovered from the fermentations contained 8.8–9.3% nitrogen. Paraffin wax also served as a suitable carbon source when dissolved in 2,6,10,14‐tertramethylpentadecane (pristane). However, substrate utilization appeared to be incomplete.
Utilization of mixed sugars in continuous fermentation. II.
Authors: Harte M. J. , Webb F. C. 
Published: December 2004

AbstractBatch growth characteristics of various organisms were determined on a number of pairs of sugars to find a stable system showing clear‐cut classical diauxie. The system selected for further study was a strain of Klebsiella (Acrobacter) aerogenes, NCIB 8021 growing on a mixture of glucose and maltose in minimal salts medium at 30°C. This showed a specific growth rate (μ) of 1.19 ± 0.03 hr.−1 on 0.01% (w/v) glucose, followed by a diauxie lag of 0.73 ± 0.04 hr and then further growth on 0.01% (w/v) maltose at μ = 0.60 ± 0.03 hr−1. This system was applied to a two‐stage continuous, stirred, aerated fermentor system, with working volumes of 1.85 and 2.77 liters, respectively, and growth was followed (mainly by optical density, referred to dry weights and viable counts) and also the concentrations of the sugars were measured. Except at the very highest flow rates, glucose was immediately and virtually completely consumed, but the utilization of maltose showed interesting variations: (a) At low feed rates between 0.09 and 0.4 vol./hr. exactly the same response was found with mixed sugars as with double concentration glucose, showing that the organism was able to metabolize maltose as well and as quickly as glucose. (b) At medium feed rates of 0.46 to 1.03 vol./hr. two deviations were observed, both of which increased as the dilution rate increased: the system showed a time lag on maltose before the cell population began to rise and the volume of medium used before the steady state was established was greater than predicted, (c) At fast feed rates, approaching “washout” condition of 1.055 to 1.135 vol./hr. the first culture vessel showed no reaction to a step change which included maltose, although, of course, with doubled glucose it responded immediately. The second vessel, however, quickly metabolized the overflow maltose, and showed a steady increase of cell population to the theoretical steady state. These results may have significance for industrial systems using complex commercial substrates.