bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of strongly NLO‐active molecularly‐based ferromagnets
Authors: Bénard Sophie , Yu Pei , Coradin Thibaud , Rivière Eric , Nakatani Keitaro , Clément René
Published: December 2004

Molecule‐based ferromagnets that exhibit strong second‐harmonic generation (SHG) are presented here for the first time. The strategy for producing such materials—replace the “innocent” bulky cations (C) in the C[M′M(ox)3] family of bimetallic magnets (M′ is e.g. Mn and M = CrIII or FeIII; the Figure shows the structure) by hyperpolarizable cationic chromophores—is described and X‐ray, magnetic, and SHG results are reported.

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Planar pore‐filling — adsorption in porous silicon
Authors: Bjorklund Robert B. , Zangooie Shahin , Arwin Hans
Published: December 2004

Porous silicon has potential applications not only in optoelectronics but also in the areas of sensors and biomaterials. Research in this direction relies on the sorptive properties of the material, which means that fundamental adsorption studies are important. The various pore morphologies of porous silicon are reviewed, as are the types of experiments that have been performed related to adsorption from the gas and liquid phases, along with their results. It is suggested that three‐dimensional surface‐physics‐oriented studies would lead to interesting insights.
Industrial chemistry in the information age
Authors: Kleemann Axel
Published: December 2004

Ullmann's Encyclopedia of Industrial Chemistry has a long tradition, going back to 1914, when the first German edition was published. How has this important publication, known by chemists throughout the world—not just in German‐speaking countries—as an important source of reliable information, adjusted to changing times? How has it managed the transition to the electronic information age? These questions are answered by Professor Axel Kleemann, a member of the Editorial Board of Ullmann's, who also looks at the advantages offered by the new CD‐ROM version.
Excellent gelators for organic fluids: Simple bolaform amides derived from amino acids
Authors: Hanabusa Kenji , Tanaka Reo , Suzuki Masahiro , Kimura Mutsumi , Shirai Hirofusa
Published: December 2004

The gelation of organic solvents by low molecular weight gelators is an area of study still in its infancy. Difficulties in the design of universal gelators suitable for a wise variety of liquids arise because the self‐aggregation of teh molecules strongly depends on the polarity of the solvent. The bolaform amides presented, derived from N‐protected amino acids, are demonstrated to have gel‐forming abilities for a range of organic solvents. The driving force responsible for gelation in this case is suggested and it is proposed that the amides form an extended molecular sheet in the liquids.
Self‐assembled PAMAM dendrimer films
Authors: Evenson Simon A. , Badyal Jas Pal S.
Published: December 2004

Self‐assembly of starburst dendrimers into closely packed cells (see the optical micrograph in the Figure) is reported for generation 9.5 polyamidoamine (PAMAM) dendrimers solvent‐cast onto hydrophilic silicon substrates. It is shown that on the microscopic scale the cells are made up of a complex network of intertwined dendritic microfibrils. Potential applications of such novel surfaces are suggested.

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Encapsulated electroactive molecules
Authors: Gorman Christopher B.
Published: December 2004

The role of a dendrimer as an encapsulating shell around small molecules or the dendrimer core itself are briefly outlined. It is shown that encapsulation by a dendrimer reduces the rate of electron transfer to or from a redox‐active moiety incorporated in the core according to the degree of branching around the core. Development of this idea could lead to a molecular switch or an information storage device. The use of the properties of the core in order to obtain information about the shape, internal organization, and environment within a dendrimer is also outlined and an example given.
Aligned aluminophosphate molecular sieves crystallized on floating anodized alutnina by hydrothermal microwave heating
Authors: Tsai Tzeng‐Guang , Chao Kuei‐Jung , Guo Xing‐Jian , Sung Shing‐Li , Wu Chih‐Ning , Wang Yuh‐Lin , Shih Han‐Chang
Published: December 2004

Thin films of aligned zeolite crystals can significantly improve the quality of advanced materials prepared using zeolites as a nanostructured host. A membrane of vertically aligned aluminophosphate molecular sieves is prepared on floating anodized alumina using microwave heating. The Figure shows the first step in the proposed synthetic scheme—preformed nuclei penetrate the cylindrical nanochannels of the alumina substrate.

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Photodiode performance and nanostructure of polythiophene/C60 blends
Authors: Roman Lucimara S. , Andersson Mats R. , Yohannes Teketel , Inganás Olle
Published: December 2004

Highly efficient photovoltaic devices, constructed using polythiophene derivatives blended with fullerenes, are described. The photovoltaic behavior of the sandwich‐structure devices (current‐voltage characteristic, conversion efficiency) is reported and the electrical, optical (optical absorption, photoluminescence), and morphological properties of the blends are presented. The importance of the morphology of the films is pointed out: it can determine the photovoltaic properties of the devices.
Wire formation on circuit boards using spatially coupled bipolar electrochemistry
Authors: Bradley Jean‐Claude , Crawford Jeffrey , Ernazarova Karima , McGee Michael , Stephens Samuel G.
Published: December 2004

The creation of electrical contacts between selected copper rings on a commercial circuit board by a novel method is reported. The method relies on spatially coupled electrodissolution and electrodeposition mediated by an electric field, followed by electroless deposition. The Figure shows an example of a conductive wire formed between two circular rings after the electroless plating step—see also the cover of this issue.

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Organoporous hosts with adjustable molecular environments
Authors: Swift Jennifer A. , Russell Victoria A. , Ward Michael D.
Published: December 2004

Tailored organoporous materials—the organic counterparts to inorganic nanoporous materials–have been prepared by a design strategy based on the observation that guanidinium organosulfonates (C(NH2)3⊕RSO3⊖) crystallize predictably in layered structures. The extension to disulfonates is shown to produce, among others, the motif shown in the Figure (the ovals are organodisulfonate pillars and the rectangles, guests).

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A heat‐resistant silicon‐based polymer
Authors: Itoh Masayoshi , Inoue Kohji , Iwata Kenji , Ishikawa Junichi , Takenaka Yoshihiro
Published: December 2004

Materials combining the best properties of plastics and ceramics, i.e., that are as heat and combustion resistant as ceramics and as moldable and light as plastics, would find many applications. As a step in this direction, the preparation and properties of a silicon‐based organic polymer, MSP, which includes the Si(H)–C unit, and related polymers are described. MSP's extremely high temperature of 5% weight loss (860°C) indicates that further investigation of polymers containing the Si(H)–C unit could be fruitful.
Glioma therapy and real‐time imaging of neural precursor cell migration and tumor regression
Authors: Shah Khalid , Bureau Emilie , Kim Dong‐Eog , Yang Katherine , Tang Yi , Weissleder Ralph , Breakefield Xandra O.
Published: December 2004

Despite many refinements in current therapeutic strategies, the overall prognosis for a patient with glioblastoma is dismal. Neural precursor cells (NPCs) are capable of tracking glioma tumors and thus could be used to deliver therapeutic molecules. We have engineered mouse NPCs to deliver a secreted form of tumor necrosis factor–related apoptosis–inducing ligand (S‐TRAIL); S‐TRAIL is optimized to selectively kill neoplastic cells. Furthermore, we have developed means to simultaneously monitor both the migration of NSCs toward gliomas and the changes in glioma burden in real time. Using a highly malignant human glioma model expressing Renilla luciferase (Rluc), intracranially implanted NPC‐FL‐sTRAIL expressing both firefly luciferase (Fluc) and S‐TRAIL was shown to migrate into the tumors and have profound antitumor effects. These studies demonstrate the potential of NPCs as therapeutically effective delivery vehicles for the treatment of gliomas and also provide important tools to evaluate the migration of NPCs and changes in glioma burden in vivo. Ann Neurol 2005;57:34–41
Interleukin‐1β contributes to the generation of experimental febrile seizures
Authors: Dubé Celine , Vezzani Annamaria , Behrens Marga , Bartfai Tamas , Baram Tallie Z.
Published: December 2004

Fever can provoke “febrile” seizures (FS). Because complex FS may promote development of temporal lobe epilepsy, understanding their mechanisms is clinically important. Using an immature rodent model and transgenic technology, we examined the role of interleukin‐1β, (IL‐1β), a pyrogenic, proinflammatory cytokine, in FS. IL‐1β receptor–deficient mice were resistant to experimental FS. This resistance appeared independent of genetic background and was attributed to lack of IL‐1β signaling, because exogenous cytokine reduced seizure threshold in wild‐type but not receptor‐deficient mice independent of strain. In addition, high IL‐1β doses induced seizures only in IL‐1β receptor–expressing mice. These data indicate that IL‐1β signaling contributes critically to fever‐induced hyperexcitability underlying FS, constituting a potential target for their prevention. Ann Neurol 2005;57:152–155

An Erratum has been published for this article in Ann Neurol 57: 609, 2005.
Pick bodies in a family with presenilin‐1 Alzheimer's disease
Authors: Halliday Glenda M. , Song Yun Ju C. , Lepar Gila , Brooks William S. , Kwok John B. , Kersaitis Cindy , Gregory Gillian , Shepherd Claire E. , Rahimi Farid , Schofield Peter R. , Kril Jillian J.
Published: December 2004

Presenilin‐1 (PS‐1) mutations can cause Pick's disease without evidence of Alzheimer's disease (AD). We describe a family with a PS‐1 M146L mutation and both Pick bodies and AD. Sarkosyl‐insoluble hyperphosphorylated tau showed three bands consistent with AD, although dephosphorylation showed primarily three‐repeat isoforms. M146L mutant PS‐1 may predispose to both Pick's disease and AD by affecting multiple intracellular pathways involving tau phosphorylation and amyloid metabolism. Ann Neurol 2005;57:139–143
Band centrifugation of macromolecules in self‐generating density gradients. II. Sedimentation and diffusion of macromolecules in bands
Authors: Vinograd Jerome , Bruner Robert
Published: December 2004

Three approaches to the simultaneous sedimentation and diffusion of hands or zones of noninteracting homogeneous macromolecules are examined: (1) The authors' method of moments: (2) the transport me of Sehumaker and Rosenbloom; and (3) the stochastic solution of the Lamm equation due to Gehatia and Katehalski. All three methods indicate that the motion of the maximum of the hand may be used to evaluate the sedimentation coefficient. The moment, method provides relations which appear to be useful for measuring diffusion coefficients. Relations are given for the analysis of resolved components. The problem of measuring sedimentation coefficients of macromolecules with concentration‐dependent sedimentation coefficients is examined. Methods are described for evaluating the sedimentation coefficient in these systems and for obtaining the sedimentation coefficient at infinite dilution. Methods are described for determining the weight‐average sedimentation coefficient in Multi‐component systems, and the differential and integral distribution of sedimentation coefficients of macromolecules with low‐diffusion coefficients.
Charge density on native and ultraviolet‐irradiated myosin A
Authors: Westley Francis , Kaldor George , Cohen Irving
Published: December 2004

The axial ratios (a/b) of native and 60 min. ultraviolet‐irradiated myosin A molecules were calculated from previously reported sedimentation and diffusion data; values found were a/b = 74, a = 1880 A., and b = 26 A. for native myosin A; a/b = 104, a = 3280 A., and b = 32 A. for 60 min. ultraviolet‐irradiated myosin A. Electrophoretic mobilities gave identical values of 3.2 (±0.1) × 10−5 cm.2/v.‐sec. for both native and 60 min. ultraviolet‐irradiated myosin A. From the prior sedimentation and diffusion data, together with newly obtained electrophoretic data, the net charge Z and the charge density σ of native and ultraviolet‐irradiated myosin A molecules were calculated from Henry's equation. The following results were obtained: for native myosin A, Z = 160 negative charges per molecule and σ = 22 coulombs/cm.2; for ultraviolet‐irradiated myosin A, Z = 312 negative charges per molecule and σ = 20 coulombs/cm.2. The results of this study provide an experimental demonstration that, the electrophoretic mobility of charged solute particles is dependent upon the particle charge density and not on the absolute charge of the particle.
Differential thermographic features of some crystalline biopolymers
Authors: Morita Hirokazu
Published: December 2004

Crystalline proteins, nucleic acids, nucleotides, and nucleosides have been examined by differential thermal analysis. Characteristic thermograms are illustrated for globular, serum, and blood plasma proteins, calf thymus DNA, sodium triticonucleate, sodium thymonucleate, sperm DNA, yeast RNA, adenosine‐3′‐phosphate, adenosine‐5′‐phosphate, disodium adenosine triphosphate, adenosine, and deoxyadenosine. A pronounced effect of moisture on the differential thermal properties of DNA has been observed. It is suggested that solid‐state denaturation is one of the prominent thermal effects recorded by the differential thermal analysis of proteins and nucleic acids.
Studies on nucleic acids. VIII. Changes in the stability of DNA secondary structure by interaction with divalent metal ions
Authors: Venner H. , Zimmer Ch.
Published: December 2004

The melting temperature of a natural DNA is decreased in the presence of increasing amounts of copper ions, whereas other divalent metal ions stabilize the DNA secondary structure at low ionic strength. At 1.28 × 10−4M, Cu2+ produces a decrease of Tm depending on base composition. At very low Cu2+ concentrations (0.5 Cu2+/2 DNA‐P) a stabilization of the DNA conformation appears due to an interaction between Cu2+ and phosphate groups of the DNA molecule. In this case the normal trend of GC dependence of Tm exists similar to that with Na+ and Mg2+ as counterions. If copper ions are in excess, the observed destabilization is stronger for DNAs rich in guanine plus cytosine than for those rich in adenine plus thymine. A sharp decrease of Tm occurs between 0.5–0.8 Cu2+/2 DNA‐P and 1.5 Cu2+/2 DNA‐P. The breadth of the transition decreases at high Cu2+ concentration with further addition of copper ions. Denaturation and renaturation experiments indicate that Cu2+ ions exceeding the phosphate equivalents interact with the bases and reduce the forces of the DNA helix conformation. Evidence is presented, that the destabilization effect produced by Cu2+ is possibly due to an interaction with guanine sites of the DNA molecule.
Interaction of polynuclear aromatic hydrocarbons, 4‐nitroquinoline 1‐oxides, and various dyes with DNA
Authors: Nagata Chikayoshi , Kodama Masahiko , Tagashira Yusaku , Imamura Akira
Published: December 2004

By using the flow dichroism method, in vitro interaction of the aromatic polynuclear hydrocarbons with calf thymus DNA was studied. A clear dichroism of the hydrocarbons which interacted with DNA was observed, showing a specific type of interaction. Hydrocarbons were classified into two groups, depending on whether the orientation is parallel or perpendicular to the direction of flow. 3,4‐Benzopyrene, pyrene, and phenanthrene belong to the first group, and the second group contains 20‐methylcholanthrene, tetracene, pentacene, and coronene. 4‐Nitroquinoline 1‐oxide (4‐NQO) and its derivatives have also been found to be oriented parallel to the planes of bases of DNA, and a distinct parallel was found between the amount of binding and carcinogenicity. Base specificity of binding of 4‐NQO with DNA‐was studied, and purines were suggested to be active sites of interaction. Actinomycin D, several acridine dyes, and methylene blue etc. were found to be oriented parallel to the planes of DNA bases, and in the cases of acridine dyes this finding does not contradict the intercalation mechanism proposed by Lerman.
Numerical solutions of the Lamm equation. I. Numerical procedure
Authors: Dishon Menachem , Weiss George H. , Yphantis David A.
Published: December 2004

This paper gives an account, of the numerical technique used to derive results to he presented in future papers of this series.
Electric properties of macromolecules. IX. Dipole moment, polarizability, and optical anisotropy factor of collagen in solution from electric birefringence
Authors: Yoshioka Koshiro , O'konski Chester T.
Published: December 2004

The electric birefringence of collagen solutions has been measured over a wide range of field strength with the pulse technique. The soluble collagen was from rat tail tendon. The solvent used was dilute acetic acid. Very pronounced saturation of the electric birefringence was observed, permitting calculation of the optical anisotropy factor. The Kerr constant was determined by extrapolation to zero field strength. From the dependence on field strength of the birefringence, the permanent dipole moment and the anisotropy of polarizability were separately determined. The contribution of the former to the Kerr constant was found to be twice as large as that of the latter. The same conclusion was obtained from the initial slope of the rise curves of the birefringence at low fields. The permanent dipole moment was 1.5 × 104 Debye, and the anisotropy of polarizability was about 3 × 10−15 cm.3. The magnitude of the latter indicates that the ion atmosphere polarization is important. Effects of added salt and thermal denaturation on the electric birefringence were explored.
Circular dichroism measurements of benzyl L‐aspartate–nitrobenzyl L‐aspartate copolymers and their use in detecting and characterizing preferred polymer conformations
Authors: Bradley Dan F. , Goodman Murray , Felix Arthur , Records Ruth
Published: December 2004

We have examined the nature of the circular dichroism band at 330 mμ for a series of copolymers of β‐p‐nitrobenzyl L‐aspartate with β‐benzyl L‐aspartate. The circular dichroism band arises from an electronic transition in the nitroaromatic group. In order to interpret the effect quantitatively, we employed a simplified statistical treatment and curve fitting for six copolymers. Both approaches gave consistent results, which indicates that the dichroism comes from pairwise interactions between two nitrobenzyl groups. We constructed a molecular model that meets the constraints and requirements of the analyses developed in this paper. In this model, it is proposed that the main chain forms a right‐handed α‐helix and that nitrobenzyl groups separated by four residues interact with each other.
The V amylose–water system: Enthalpy of hydration on the helix exterior
Authors: Nicolson P. C. , Yuen G. U. , Zaslow B.
Published: December 2004

The reaction, V amylose hydrate ⇄ H2O + V amylose dehydrate, where the amylose hydrate and dehydrate are pseudohexagonal, helical species with packing diameters of 13.7 and 13.0 A., respectively, has been studied. The V amyloses were exposed to water vapor pressures at various temperatures, with phase determination obtained by identifying solid reactant and product from their x‐ray patterns. Reversibility of reaction was found to occur over a 50–96°C. range. A Clausius‐Clapeyron plot yields a ΔH of reaction of 10.4 kcal./mole of water released, which value is close to analogous heats of reaction of many common hydrate systems.
Nature of Cu(II)‐poly(glutamic acid) complex in aqueous solution
Authors: Takesada Hiroko , Yamazaki Hideo , Wada Akiyoshi
Published: December 2004

Complex formation of poly(glutumic acid) with cupric ions in aqueous solution was investigated by three different methods: optical spectroscopy, optical rotatory dispersion, and electron spin resonance. Formation of a characteristic complex was found to occur in a pH region suitable for the helix‐coil transition. An analysis of the ESH spectrum of the complex is given, and the results of calculation of bonding parameters suggest that the bond between copper and nitrogen atoms had an appreciably covalent character. The change in the secondary structure of the polymer as a result of complex formation is discussed.
Base composition of intact nucleic acid oligomers
Authors: Mandeles Stanley , Cantor Charles R.
Published: December 2004

The base composition of intact, purified, oligonucleotides has been determined by comparing the absorption spectrum of each oligomer with calculated curves. The spectral curve of each oligomer was measured in 7M urea at three pH values and digitized at 1‐mμ intervals. The calculated curves consisted of the sums of the absorption spectra of mononucleotides in 7M urea at the same pH's. A computer was used to make the comparisons and establish the best fit. Results are presented for nine of the ten possible dimer composition isomers; trimers from pancreatic and T1 ribonuclease hydrolyzates of TMV‐RNA; poly‐A, poly‐C, and poly‐U; and intact tobacco mosaic virus‐RNA.
Validity of the “two‐state” hypothesis for conformational transitions of proteins
Authors: Lumry Rufus , Biltonen Rodney , Brandts John F.
Published: December 2004

The theory, character, and properties of cooperative transitions are developed with special reference to the abrupt changes of state which occur in protein solutions. Comparisons of helix–coil processes and protein conformational reactions show that though cooperation dominates both of these processes, there are important differences. Tests of two types for the validity of the two‐state approximation are presented with specific applications to proteins. Available experimental evidence demonstrates that the thermally induced reversible transitions of ribonuclease, α‐chymotrypsin, and chymotrypsinogen A under conditions thus far examined are two‐state processes.
The helix–coil transformation for tropocollagen solutions and its relationship to transformations involving the crystalline form of the protein
Authors: Bianchi Estella , Conio Giuseppina , Ciferri Alberto
Published: December 2004

Collagen molecules can exist, in the aggregate crystalline state (C) and in solutions, as tropocollagen helices (H) or random coils (RC). We have compared the role of temperature, salt type, and salt concentration, C8, on the transformations: C → RC (I), H → RC (II), and H → C (III) under near‐isoelectric conditions. Processes I and II occur in the direction from ordered to disordered form on increasing temperature, while process III occurs in the direction crystal → dissolved helices on lowering temperature. The order of both anions and cations for increasing the stability of the dissolved random coiled form is similar for processes I and II, but the order of the anions for increasing the stability of the dissolved helices, according to process III, is reversed with respect to the Hofmeister series. TI and TII are greatly and continuously depressed by some salts on increasing C8 while, for other salts, they are at first slightly depressed and then raised. TIII, instead, is at first raised and then lowered on increasing C8. For a given salt the field of stability of each form is determined, on a pseudo‐phase diagram, by the relative positions of the TI versus C8, the TII versus C8, and the TIII versus C8, curves. The similarity of the effect of temperature, salt type, and concentration on processes I and II supports the contention that both processes are controlled by the interaction of the random coiled form with the salt solution. The phenomenon of crystallization by increasing temperature is complicated by large time effects and, often by lack of reversibility. Assuming, nevertheless, that there is an underlying equilibrium process, two possible interpretations are proposed. The peculiar trend of the TIII versus C8 curve is justified on the basis that it reflects the usual change from salting in to salting out on increasing C8, allowing for the fact that the dissolved phase is stable in the low‐temperature range. The reversal of the order of anions for process III can be most simply justified in terms of the slight cat ionic character of the tropocollagen units. Accordingly, the dissolved helices will be more; stable of the crystalline form depending upon the occurrence of a net charge different from zero on the protein, as well as upon low ionic strength and low temperature. Minute alterations of KCl concentrations are able to cause isothermal precipitation of fibers and probably constitute a controlling factor for the fibrogenesis in vivo.
Structure and optical activity of the DNA–aminoacridine complex
Authors: Gardner B. J. , Mason S. F.
Published: December 2004

The electronic absorption and circular dichroism spectra of the DNA‐acridine orange complex have been measured over a range of ionic strength, pH, and DNA phosphate to dye (P/D) ratios. Three circular dichroism bands associated with the long wavelength absorption band of acridine orange are induced on complex formation with DNA. Two of the dichroism bands, due mainly to dimeric dye molecules, are favored by low ionic strength, low pH (3.2), and a low P/D ratio (∼3), while the third, deriving primarily from monomeric dye, is optimum at high ionic strength, neutral pH, and a larger P/D ratio (9). The data suggest that monomeric acridine orange binds to DNA in the form of a left‐handed helical array with four dye molecules per turn, while the bound dimer has a skewed sandwich conformation which is itself dissymmetric. The stereochemical relations between the bound monomer dye and the DNA are consistent with a modified intercalation model for the DNA‐acridine complex.
Interaction of spermine and DNA
Authors: Hirschman Shalom Z. , Leng Marc , Felsenfeld Gary
Published: December 2004

The effect of spermine upon the denaturation temperature (Tm) of DNA's of various base compositions has been found to depend upon both the base composition of the DNA and the pH of the solution. Measurement of the hydrogen ion titration curve of spermine as a function of temperature reveals that the net charge of the spermine molecule is undergoing a rapid change with temperature in the range of temperatures at which DNA denatures. Since the value of Tm depends upon base composition, the correlation of the effect of spermine upon Tm with the base composition of the DNA used may be explainable in terms of the changing degree of ionization of spermine. The binding of spermine to native DNA has also been studied by dialysis equilibrium. There is no significant variation either in the number of strongly binding sites or strength of binding with base composition. It is concluded that there is no evidence of correlation between the binding of spermine and the base composition of DNA.
Extrinsic cotton effects of proflavine bound to polynucleotides
Authors: Blake A. , Peacocke A. R.
Published: December 2004

The magnitude of the Cotton effect of proflavine which is bound to RNA or to denatured DNA depends on the ratio of bound proflavine to nucleic acid base. A statistical treatment which explains this behavior has been fitted to the experimental curves and indicates that optical activity arises through interaction between two or more bound proflavine molecules. The corresponding requirement with double helical DNA is for interaction between 3–4 proflavine molecules. Although proflavine binds to denatured DNA at pH 2.8, as shown by the shift of the proflavine spectrum, the strong binding process is absent, and to this is attributed the absence of the Cotton effect at low pH. Studies on the Cotton effects of proflavine bound to poly A and poly U at neutral pH, to poly A at acid pH and to poly (A + U) allow the generalization that a relatively rigid configuration of the binding macromolecule is required for the induction of these extrinsic Cotton effects.
Interaction between proteins and salt solutions. IV. Enrichment of salts in collagen during denaturation
Authors: Ciferri A. , Garmon R. , Puett D.
Published: December 2004

Using 14C‐labeled KSCN and 36Cl‐labeled KC1, we have determined the selective removal of ions and water by fibrous, crosslinked collagen both below and above the denaturation temperatures at several molarities under or near isoelectric conditions. The results for KSCN show there is an increase in ion binding at the denaturation temperature. These data, in conjunction with date from the literature, have been used to evaluate binding constants and mole fractions of available binding sites, as well as the free energy of binding various salts to collagen and gelatin. The values so obtained correlate satisfactorily with similar quantities obtained from the experimental dependence of the shrinkage temperature of collagen on salt concentration using a simple theory for the melting point depression which includes the effect of binding in the denatured state. Salting‐out agents show negligible binding to the protein, and this confirms the earlier finding that the interaction between these agents and the protein can be approximately described by conventional polymer–diluent theories which do not consider ion binding. Also, an analysis of the role of unequal anion and cation binding is presented.
On the two kinds of nucleation in the helix–coil transition theory of polypeptide chains
Authors: Bixon M. , Lifson S.
Published: December 2004

The nucleation of a helical sequence from a random chain of the polypeptide molecule as well as the nucleation of a random‐coil sequence from the helical conformation of the molecule are considered simultaneously in evaluating the partition function of the system. This partition function is then used for a comparative analysis of the theories of Zimm and Bragg, Gibbs and DiMarzio, and Lifson and Roig. It is shown that while all three account properly for the essential nature of the nucleation phenomenon the first considers in detail the random‐coil nucleation, the second emphasizes the details of the helix nucleation, while the third neglects the fine details of both in a symmetric way.
Chemical synthesis of a dextran model, poly‐α‐(1 → 6)‐anhydro‐D‐glucopyranose
Authors: Ruckel Erwin R. , Schuerch Conrad
Published: December 2004

Poly‐α‐(1 → 6)‐anhydro‐D‐glucopyranose has been synthesized by the phosphorus pentafluoride‐catalyzed polymerization of l,6‐anhydro‐2,3,4‐tri‐O‐benzyl‐β‐D‐glucopyranose and subsequent debenzylation. Physical characterization establishes its high polymeric character and stereoregularity.
Structure and stability of complexes formed by nucleic acids. I. Binding of acridine to DNA
Authors: Bleaks D. J. , Danyluk S. S.
Published: December 2004

Nuclear magnetic resonance spectra of acridine have been measured in aqueous methanol solutions over a wide concentration range in the presence and absence of dissolved DNA. In solutions containing DNA the acridine spectra show a marked line broadening and intensity decrease at temperatures lower than 50°C. These line‐shape changes can be associated with two types of binding interactions: (1) a tight, irrotational binding of the acridine at low acridine:phosphate ratios and (2) a weaker, rotationally less restrictive binding at high acridine concentrations. At temperatures above 50°C. a marked line narrowing is noted for the acridine spectrum and is attributed to an increase in mobility of the bound acridine as the DNA complex undergoes a helix–coil transition. A loose association of acridine molecules with the purine and pyrimidine bases in heat‐denatured DNA is indicated by chemical shift changes in the acridine spectrum. The NMR measurements also show that the presence of acridine in denatured DNA solutions greatly reduces renaturation of the DNA.
Application of matrix rank analysis to the optical rotatory dispersion of TMV RNA
Authors: McMullen D. W. , Jaskunas S. R. , Tinoco Ignacio
Published: December 2004

The method of matrix rank analysis has been applied to a large body of experimental data to determine and identify the minimum number of independent spectral components that, were contained within it. The optical rotatory dispersion of TMV RNA was measured in the wavelength region 230–350 mμ, for a wide range of temperatures and ionic strengths. Over the whole range of conditions considered, the observed optical rotatory dispersion spectra were found to be a superposition of two basic spectra only. Evidence is put forward relating these spectra to the single‐strand and double‐strand helical forms of the molecule. A model is proposed to explain the observed spectral changes in terms of an equilibrium between these two conformations, which leads to a direct calculation of the percentage composition of the double strand at any of the conditions considered. This equilibrium, while simple in general description, appears multi‐state and complex in detail. This method of analysis is both powerful and of wide applicability, since it is independent of the source of the data.
Volume changes accompanying collagen denaturation
Authors: Christensen R. G. , Cassel J. M.
Published: December 2004

A dilatometric technique is employed to measure the volume changes occurring on denaturation of collagen solutions and tendons. Partial specific volumes of tropocollagen are calculated to be 0.686 ml./g. in water and 0.689 ml/g in 0.1M citrate buffer. From data on non‐aqueous solutions, it is estimated that most of the volume change arises from changes in polymer configuration rather than from changes in solvation.
Effect of superhelical structure on the secondary structure of DNA rings
Authors: Glaubiger Daniel , Hearst John E.
Published: December 2004

A quantity, called the linking number, is defined, which specifies the total number of twists in a circular helix. The linking number is invariant under continuous deformations of the ring and therefore enables one to calculate the influence of superhelical structures on the secondary helix of a circular molecule. The linking number can be determined by projecting the helix into a plane and counting strand crosses in the projection as described. For example, it has been shown that for each 180° twist in a left‐handed superhelix, a right‐handed 360° twist is removed from the secondary helix, thus allowing local unwinding.
Infrared studies of deoxyribonucleic acids, their constituents and analogues. II. Deoxyribonucleic acids with different base composition
Authors: Fritzsche H.
Published: December 2004

The base composition of DNA from microorganisms varies over a wide range of guanine + cytosine (G‐C) content. We have examined the infrared spectra of a number of DNA samples isolated from different microorganisms and have found marked differences in their infrared spectra. These differences have been related to the G‐C content of the investigated DNA samples. A comparison between the infrared spectra of nucleosides, synthetic polynucleotides, apurinic acid, and apyrimidinic acid has permitted a more extensive assignment of infrared bands to distinct base residues. The relative intensity of the absorption bands at 1485 and 1505 cm.−1 depends on the G‐C content of the deuterated DNA sample. On the basis of these results a new method for the determination of the G‐C content in DNA has been developed from the results. Its advantage is that the measurement is rapid and the DNA samples are not changed by the procedure.
The circular dichroism spectrum of poly‐L‐acetoxyproline
Authors: Bovey F. A. , Hood F. P.
Published: December 2004

We report the circular dichroism (CD) spectrum of poly‐Lacetoxyproline in trifluoroethanol, a solvent in which the form I to form II conformational isomerization occurs slowly enough to permit observation of the spectral changes. A comparison is made to poly‐Lproline. As judged by the similarity of the CD spectra, the conformations of the corresponding forms of the two polymers must be nearly the same. Transition assignments are proposed; these are shown to agree with the theoretical calculations of Pysh. There is a serious unexplained discrepancy between our solution data and those of Fasman for poly‐Lacetoxyproline.
Noncomplementarity in base sequences between the cohesive ends of coliphages 186 and λ and the formation of interlocked rings between the two DNA's
Authors: Wang James C. , Schwartz Harley
Published: December 2004

The half molecules of 186 DNA have been isolated by the Hg(II)–Cs2SO4 density gradient centrifugal ion technique. The buoyant densities of the two halves in CsCI at 25°C. are 1.713 and 1.709 g./cm.3, corresponding to GC contents of 54% and 50%, respectively. Similarly, 5‐bromouracil labeled λ DNA halves were separated. The isolation of the four DNA halves made it possible to test for homology in base sequences between the cohesive ends of λ and those of 186. There was no indication of any significant homology in base sequences between the cohesive ends of the two DNA's, as indicated by the absence of a band with intermediate buoyant density in CsCI when either half of 186 DNA was annealed with either half of 5‐bromouracil labeled λ DNA and then centrifuged. The lack of cohesion between the two DNA's made it possible to demonstrate unequivocally the formation of interlocked rings (catenanes) between the two DNA's. The existence of a dimeric catenane is evidenced by the formation of a species of intermediate buoyant density when 5‐bromouracil labeled λ DNA is cyclized in the presence of cyclic 186 DNA of a relatively high concentration. The molecular weight of one DNA relative to the other can be calculated from the position of the dimeric catenane in a density gradient by using the method of Baldwin. The result was in complete agreement with our previous measurements from the sedimentation coefficients and by electron microscopy. The probability of dimeric catenane formation when one DNA is cyclized in the presence of another DNA is discussed. The experimental results agree with the theoretical expectation.
Conformational studies on poly‐L‐tryptophan: Circular dichroism and X‐ray diffraction studies
Authors: Peggion E. , Cosani A. , Verdini A. S. , Del Pra A. , Mammi M.
Published: December 2004

Circular dichroism (CD) measurements were carried out on various copolymers of L‐tryptophan and γ‐ethyl L‐glutamate in ethylene glycol monomethyl ether as the solvent. On increasing the L‐tryptophan content of the copolymers a gradual change in the CD spectra was observed. The typical spectrum of the right‐handedα‐helix becomes more and more evident as the L‐tryptophan content decreases. On the basis of these results we assumed that no conformational transition occurs on proceeding from pure poly (γ‐ethyl L‐glutamate) to pure poly‐L‐tryptophan in ethylene glycol monomethyl ether: therefore the conformation of poly‐L‐tryptophan should be that of a right‐handed α‐helix. Moreover we observed that the change in the CD spectra of the copolymers is gradual but not linear on increasing the tryptophan content. The deviations from linearity were attributed to interactions among side‐chain chromophores whose contributions to the optical activity are not simply additive. An x‐ray analysis carried out on oriented films of poly‐L‐tryptophan casted from solutions of the polymer in dimethylformamide shows conclusively that the solid‐state conformation of the polymer is that, of an α‐helix.
Circular dichroism of aminoacridines bound to DNA
Authors: Dalgleish D. G. , Fujita H. , Peacocke A. R.
Published: December 2004

The binding curves of 1‐, 2‐, 3‐, and 9‐aminoacridine and proflavine on native DNA and the circular dichroism (CD) spectra of the bound cations have been determined under the same conditions. The variation of the CD spectra with the amount (r) of aminoacridine bound per DNA phosphorus was of two main kinds: (1) the rotational strength of those aminoacridines which possess a 3‐amino group depended markedly on r and decreased to relatively small values (or zero) at zero r; or, (2) the rotational strength changed relatively little with r and tended to a finite value at zero r. The relevance of these observations is discussed with respect to interelation models of the complexes and with respect to possible explanations of the basis of this induction of optical activity.
Mechanochemical melting of collagen fibers. III. Cooperativity induced by crosslinking
Authors: Yonath J.
Published: December 2004

Mechanical inciting experiments performed on collagen fibers were used to study the effect of crosslinking on contraction kinetics. With the aid of a two‐state model it is shown that the degree of cooperativity of this dematuration process is increasing with the degree of crosslinking.
Synthesis and characterization of a spin‐labeled aminoacyl transfer ribonucleic acid
Authors: Kabat David , Hoffman Brian , Rich Alexander
Published: December 2004

Unfractionated yeast transfer ribonucleic acid (tRNA) was reacted in aqueous acetone solution with the sulfhydryl spin‐labeling reagnent, N‐(l‐oxyl‐2,2,5,5‐tetramethyl‐3‐Pyrrolidinyl)iodoacetamide. Whereas tRNA stripped of amino acids reacted only slowly, there were sites on tRNA charged with cysteine which combined rapidly with the reagent. The latter class of spin‐label was quickly cleaved from the tRNA upon incubation in mildly alkaline solution (pH 8.0), suggesting that it was attached to the cysteinyl side chains. The paramagnetic resonance spectrum of column‐purified spin‐labeled cysteinyl tRNA showed that the spin‐label was partially immobilized as a result of its interaction with the tRNA. When the tRNA was slowly heated, an abrupt increase occurred in the rotational mobility of the paramagnetic amino‐acid side chain.
Theory of chromatography of macromolecules with rigid structures on hydroxyapatite columns. II. Dynamic part
Authors: Kawasaki Tsutomu
Published: December 2004

In the second or dynamic part of a theory for the chromatography of rigid macromolecules on hydroxyapatite columns the adsorption and the desorption of macromolecules were studied as a function of their position on the column and of time, the phosphate concentration also being a function of position and time. Theoretical chromatograms for model macromolecules were calculated.
Vibrational frequencies and modes of α‐helix
Authors: Itoh Koichi , Shimanouchi Takehiko
Published: December 2004

Dichroic properties of the far‐infrared absorption bands of the right‐handed α‐helix of poly‐L‐alanine were measured. The normal vibration frequencies of this structure were calculated. The assignments of bands were made and the vibrational modes dis‐cussed. The frequencies of the α‐helix vibrations with various phase differences were calculated. The frequencies of accordionlike vibrations and Young's modulus of the α‐helix were estimated. The vibrational frequency for the right‐handed α‐helices of poly‐D‐alanine and poly(L‐α‐amino‐n‐butyric acid) were calculated, and the results were used for the interpretation of the spectra of copoly‐D,L‐alanines and poly(L‐α‐amino‐n‐butyric acid). For the latter compound the existence of the rotational isomers in the side chain was strongly suggested. The vibrational modes of the bands characteristic of the α‐helix were discussed with regard to the results of the normal coordinate treatment.
Physicochemical analysis of (Pro‐Pro‐Gly)n with defined molecular weight–temperature dependence of molecular weight in aqueous solution
Authors: Kobayashi Yuji , Sakai Rume , Kakiuchi Kinji , Isemura Toshizo
Published: December 2004

Sequenced polytripeptides, (Pro‐Pro‐Gly)n, (n = 10, 15, 20), with defined molecular weights were synthesized by the solid‐phase method. Conformational changes of these sample as a function of temperature were studied by measurements of optical rotation and sedimentation equilibrium. The temperature dependence of optical rotation was shown similar to thermal transition of collagen molecule. Each of these polymers existed as a timer at lower temperature. (Pro‐Pro‐Gly)10 existed as a monomer at higher temperature, and the others were expected to behave analogously.
On the controversy over “fast” and “slow” helix–coil transition rates in polypeptides
Authors: Ullman Robert
Published: December 2004

The controversy over “fast” and “slow” helix‐coil transition rates in polypeptides is discussed. The “slow” results are derived from the assumption that multiple NMR spectra of α‐CH and NH groups arise from chemical exchange. In this paper it is shown that such spectra may be obtained without invoking chemical exchange. The multiplicity arises from the difference in helicity of amino acid residues near the ends of the chain by comparison with amino acid residues nearer the middle, and from a polydispersity in molecular weight. As a consequence of this analysis, support is given to the “fast” transition rates.
Ethidium bromide–DNA complex: Wavelength dependence of pyrimidine dimer inhibition and sensitized fluorescence as probes of excited states
Authors: Sutherland J. C. , Sutherland B. M.
Published: December 2004

Ethidium bromide inhibits the formation of ultraviolet‐induced pyrimidine dimers in DNA. The efficiency of dimer inhibition increases with increasing energy of the exciting photons. The efficiency of energy transfer from the DNA singlet to the dye singlet, as monitored by sensitized fluorescence, is independent of wavelength. The efficiency of singlet–singlet transfer agrees with that for dimer inhibition at photon energies corresponding to excitation of the lowest singlet state of DNA. Our results support a model in which dimers are formed both directly from the singlet state and also from the triplet state, with triplets arising from higher vibrational levels of the singlet.
PMR chemical shifts of TFA in poly(γ‐benzyl L‐glutamate) solutions
Authors: Liu Kang‐Jen , Lignowski S. J.
Published: December 2004

The present communication describes a new way of studying helix–random coil transformations of polypeptide, poly‐(γ‐benzyl L‐glutamate), in benzene–trifluoracetic acid (TFA) and chloroform–TFA systems. The difference between the PMR chemical shift of TFA with and without the polypeptide, measured as Δ, may be used to follow the conformational transition. This technique is particularly useful for concentrated solutions, where the PMR peaks of the polymer are so broad that no valuable information may be derived. As the TFA content increases in the system (at constant polymer concentration), Δ decreases normally whether the polymer is helical or random. However, Δ changes in a different way in the helix–random coil transition region, and actually increases with increasing TFA content. This peculiar behavior is explained in terms of the solvation of the helix and random coil structures.
Role of pH in charging of glycogen
Authors: Sterling Clarence
Published: December 2004

Glycogen acquires a negative charge in both alkaline and acidic solutions and can move in an electrical field, its mobility being related to the degree of alkalinity or acidity. There is a slight increase in relative viscosity at both ends of the pH spectrum. These effects and the changes in nuclear magnetic resonance as a function of pH are interpreted.
Preparation and properties of poly‐9‐vinyladenine
Authors: Pitha Paula M. , Pitha Josef
Published: December 2004

Poly‐9‐vinyladenine was prepared by reaction of poly‐6‐chloro‐9‐vinylpurine with ammonia and poly‐1‐vinyluracil by hydrolysis of poly‐L‐vinyl‐2‐ethoxy‐4‐pyrimidinone. In aqueous solutions poly‐9‐vinyladenine shows hypochromism in the ultraviolet spectrum and forms a complex with polyuridylic acid as detected by a further decrease in the ultraviolet absorption. Under the same conditions, poly‐9‐vinyladenine and poly‐L‐vinyluracil interact with formation of higher aggregates.