bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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

AbstractA 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

AbstractA 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

AbstractThe 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

AbstractWe 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

AbstractThe 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

AbstractCircular 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

AbstractThe 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

AbstractMechanical 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

AbstractUnfractionated 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

AbstractIn 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

AbstractDichroic 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

AbstractSequenced 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

AbstractThe 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

AbstractEthidium 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

AbstractThe 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.
Preparation and properties of poly‐9‐vinyladenine
Authors: Pitha Paula M. , Pitha Josef 
Published: December 2004

AbstractPoly‐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.
Thermal transitions in mixtures of polydeoxyribodinucleotides
Authors: Hayes F. N. , Lilly E. H. , Ratliff R. L. , Smith D. A. , Williams D. L. 
Published: December 2004

AbstractOligo d(C‐A) and oligo d(T‐G) of known average lengths, prepared by a combination of chemical and enzymatic procedures, have been mixed in 0.02 M and 0.07 M Na+, and absorbance has been studied as a function of increasing temperature. The transitions have been analyzed for the temperature of maximum slope Tm, the breadth of the transition, the value of the slope at Tm, and the maximum hyperchromicity. Linear expressions have been found relating the inverse of the length in nucleotide units (n−1) of the shorter oligomer, irrespective of its identity, to Tm and also to the transition breadth. From a difference in slope between the Tm versus n−1 expressions for the two molarities, the entropy and enthalpy of melting have been calculated as a function of n−1.
Stepwise synthesis of oligopeptides with N‐carboxy α‐amino acid anhydrides
Authors: Iwakura Oshio , Uno Keikichi , Oya Masanao , Katakai Ryoichi 
Published: December 2004

AbstractOligopeptides were synthesized in high yields by the controlled coupling reaction of N‐carboxy α‐amino acid anhydrides (NCA's) with amino acid and peptide sodium salts in the heterogeneous reaction medium of acetonitrile–water which contained sodium carbonate. In this solvent, it could be considered that the reaction could occur at the interface of acetonitrile and aqueous layers, and that NCA's could be protected by the organic layer from side reactions such as hydrolysis and polymerization. The careful control of reaction conditions such as pH of the solution was not necessary when the heterogeneous mixed solvent was used. Sodium carbonate which had not been used for a reaction of this kind could be satisfactorily used for stabilizing the carbamate intermediates in the aqueous layer of the heterogeneous reaction medium.
Heat of denaturation of lysozyme
Authors: O'Reilly J. M. , Karasz F. E. 
Published: December 2004

AbstractThe enthalpy of denaturation of lysozyme was determined by measuring the heat, capacity of an aqueous solution of this protein in the vicinity of the transition temperature, 46 °C at pH 1. Within experimental error the calorimetric, heat (56 ± 8 kcal/mole) was found to agree with the van't Hoff transition enthalpy (63 ± 6 kcal/mole) determined from optical rotation measurements as a function of temperature. This indicates that denaturation of this protein can be interpreted in terms of a two‐state model. Successive measurements of the same sample showed, from several lines of evidence, that the transition was about 80% reversible for the particular environmental conditions and thermal history involved in the study.
Transient electro‐optic Kerr effect in spheroidal particles
Authors: Wright A. Kent , Keefe William E. 
Published: December 2004

AbstractBenoit's theory of the time dependence of the birefringence transient in the Kerr cell following sudden removal of the orienting field has been examined and shown to hold only for spherical part ides and not ellipsoids of revolution. This observation is in agreement with the methods of dielectric dispersion and depolarization of fluorescence which yield two rotary diffusion constants, while Benoit's theory yields only one. A new theory is presented here which contains two rotary diffusion constants and reduces to the Benoit equation in the limiting cases of spheres and infinitely thin rods. Also the theoretical extensions of Tinoco and Ridgeway have been examined and compared to the resulting theory.
On the double peak of NMR in the helix—coil transition region
Authors: Nagayama Kuniaki , Wada Akiyoshi 
Published: December 2004

AbstractTo attempt to resolve the controversy over “fast” and “slow” helix–coil transition rates in polypeptides, nuclear magnetic resonance spectra were measured for monodisperse poly‐γ‐benzyl‐L‐glutamate (PBLG). These results were compared with simulated line spectra which were computed by taking the molecular‐weight distribution into consideration. Broad but single peaks have been observed in 220 mHz nmr for the α‐CH and NH proton resonance spectra in the transition region. The shape of the line changes with the extent of polydispersity. Assuming a fast conversion rate, a molecular model of the helix–coil transition simulates these results. Consequently, the double peak which has been observed in the nmr of polypeptides at the helix–coil transition region is shown to result from the polydispersity in molecular weight.
Interaction of metal ions with polynucleotides and related compounds. XXII. Effect of divalent metal ions on the conformational changes of polyribonucleotides
Authors: Shin Yong Ae 
Published: December 2004

AbstractChanges in the conformation of poly(G), poly(C), poly(U), and poly(I) in the presence of divalent metal ions Mg2+, Ca2+, Mn2+, Co2+, Ni2+, Cu2+, Cd2+, and Zn2+ have been measured by means of ORD and u.v. spectra. Mg2+ and Ca2+ ions stabilize helical structures of all the polynucleotides very effectively at concentrations several orders of magnitude lower than the effective concentration of Na+ion.Cu2+ and Cd2+ destabilize the helical structure of polynucleotides to form random coils. Zn2+, Ni2+, Co2+, and Mn2+ions do not behave in such a clear‐cut manner: they selectively stabilize some ordered structures, while destabilizing others, depending on the ligand strength of the nucleotide base as well as the preferred conformation of that polynucleotide.
Kinetics of thermal unfolding of lysozyme
Authors: Segawa Shin‐Ichi , Husimi Yuzuru , Wada Akiyoshi 
Published: December 2004

AbstractA reversible unfolding of lysozyme has been studied by means of the temperature‐jump method by measuring the absorbance change of pH indicator p‐nitrophenol (p‐NP). In the presence of 4.5M lithium bromide three relaxation processes were found. The fastest process with a relaxation time τ of about 30 μsec is found to come from the proton‐transfer reaction between p‐NP and His 15 in lysozyme. Only the slowest process (τ ≃ 15 sec) is a first‐order reaction and attributable to the unfolding of lysozyme. These results suggest that the all‐or‐none model can be applied to the unfolding of lysozyme as a fairly good approximation. This shows good agreement with the result of Tanford et al. (J. Mol. Biol., 15, 489 (1966); J. Mol. Biol., 73, 185 (1973)). The enthalpy, entropy, and specific heat change between a native and a denatured form are found to be close to 53 kcal/mol, 168 cal/mole/°K, and 2.1 kcal/mol/°K, respectively. The enthalpy and entropy of activation and the specific heat change for the unfolding and the folding are also obtained from kinetic experiments. In the folding reaction, the enthalpy of activation is negative. In the unfolding reaction, the specific heat change is nearly equal to zero. These results suggest that a number of intramolecular hydrogen bonds are broken, but most residues remain tightly folded in the activated state. Our results in concentrated LiBr solutions are compared with those of Tanford in concentrated GuHCl solutions.