bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proton magnetic resonance study of complex formation between N6‐methyladenosine and polyuridylic acid
Authors: Bangerter Benedict W. , Modestas Zivile 
Published: December 2004

AbstractThe interaction between N6‐methyladenosine and polyuridylic acid in D2O solution at neutral pD has been studied as a function of temperature and N6‐methyladenosine concentration by proton magnetic resonance spectroscopy. A rigid double‐stranded 1:1 complex is formed below ∼10°C, involving hydrogen‐bonded N6‐methyladenine:uracil base‐pairing and stacking of the adenine bases. This complex is less stable than the 1:2 complex formed between adenosine and polyU, and involves a more rapid exchange of the monomer between free and polymer‐bound environments.
Differences of nucleotide stacking patterns in a crystal and in binary complexes— the case of adenine
Authors: Caillet Jacqueline , Claverie Pierre 
Published: December 2004

AbstractCalculations of the intermolecular interaction energy between stacked planar molecules show that, for this type of configuration, there is no well‐defined minimum. (The energy surface exhibits a rather large flat basin and not a deep, sharply defined, minimum.) As a consequence, the relative position of the molecules is very likely to change under environmental modifications, e.g., when the molecules become part of a crystal. Detailed calculations are carried out for the case of adenine and show that the experimental structure actually displays the lowest energy among all structures tried, although no binary configuration in the crystal is identical with that giving a minimum for a binary complex. On the contrary, for a column of stacked molecules, the minimum of the total interaction energy is still practically obtained when the successive stacked pairs of the column are in the binary minimum configuration. It is concluded that, for such configurations with a loosely defined minimum like stacking, crystal structure data may be used only with great caution for assigning a precise configuration to the binary complex.
The V amylose–H2O system: Structural changes resulting from hydration
Authors: Zaslow Bert , Murphy Vincent Gerard , French Alfred Dexter 
Published: December 2004

AbstractX‐ray diffraction and stereochemical analyses were used to study the hydrated structure of the helical amylose polymorph having a fiber repeat spacing of 8 Å. Intensity calculations using computer models confirmed six as the number of residues per turn and supported the space group P212121. Both diffraction intensity and stereochemical methods indicate the suitability of residue G3 from the potassium acetate complex of cyclohexaamylose as opposed to residues with longer O(4)–O(1) vectors. Comparison of the present results with those obtained for V amylose dehydrate indicated no major conformational differences between the two helix skeletons. A net helical rotation of approximately 30° accompanied the hydrate–dehydrate transition and the rotational position in the hydrate allowed packing that was less close. Hydration water molecules were not located; noncarbohydrate peaks on the electron density maps were primarily due to Fourier series termination errors.
Dynamic light scattering studies of poly‐L‐lysine HBr in the presence of added salt
Authors: Lee Wylie I. , Schurr J. Michael 
Published: December 2004

AbstractClipped autocorrelation functions for the fluctuating intensity of light scattered from dilute solutions of poly‐L‐lysine in 0.2 M NaBr have been observed over a wide range of time scales down to 1.83 μsec, and over a wide range of pH. Two poly‐L‐lysine samples of molecular weight 35,000 and 200,000, respectively, were compared to determine the extent of draining of the so‐called random‐coil configuration. The observed correlation functions were in general very satisfactorily represented by simple translation diffusion of single molecules. At high pH ∼10–10.4, there was evidence of considerable aggregation, but no indication whatsoever of any unusually fast component, as reported recently by Jamieson et al. for poly‐L‐lysine HBr in the absence of salt.A 30% rise in the diffusion coefficient to a peak at pH 10 parallels the previously reported dip in the intrinsic viscosity, and is interpreted in terms of a more compact structure in that pH region between the coil and helix extremes.
Double‐helical DNA and RNA circular dichroism. Calculations on base–sugar‐phosphate helix interactions
Authors: Moore Dexter S. , Wagner Thomas E. 
Published: December 2004

AbstractTheoretical calculations of the near ultraviolet (uv) circular dichroism of double‐helical DNA and RNA models were performed in order to evaluate the effects, on the calculated circular dichroism, of including the interactions of near uv quantum transitions of the nucleic acid bases with classical polarizable bonds of the sugar‐phosphate backbone. Double‐helical models (A‐form, B‐form, and C‐form DNA and RNA‐11) from X‐ray diffraction data were used in the calculations. The results indicate that the contributions to the circular dichroism in the near uv region, of these types of interactions, provide calculated spectra that are slightly altered from calculated spectra when only base–base transition interactions were considered.
Synthesis and optical studies of L‐methionine oligopeptides in solution
Authors: Naider Fred , Becker Jeffrey M. 
Published: December 2004

AbstractA series of L‐methionine oligomers [BOC‐(Met)n‐OMe] (n = 2–7) and the corresponding diastereomeric di‐ and tripeptides were synthesized using the mixed anhydride method. Oligomers prepared in this manner were optically pure and were obtained in reasonable yield. Preliminary optical examination of the peptides suggests that secondary structures may begin forming in the pentamer or hexamer in trifluoroethanol. BOC‐(Met)4‐OMe and BOC‐(Met)5‐OMe were also synthesized using an insoluble resin containing BOC‐L‐methionine as the nitrophenol active ester.
Dispersion equation and polarizability of bovine serum albumin from measurements of refractive indices
Authors: Andersen M. , Painter L. R. , Nir S. 
Published: December 2004

AbstractRefractive indices of bovine serum albumin solutions in saline and in 2‐chloro ethanol are measured for the spectral region 1770–10000 Å by a reflectance method. A procedure for the determination of a dispersion formula for binary mixtures is developed and applied. The electronic polarizability of bovine serum albumin is determined and is found to be almost independent of the solvent and concentration. Hence it follows that the electronic polarizability of bovine serum albumin is almost independent of the molecular environment.
Optical rotatory properties of L‐cystine conformational isomers. Theoretical analysis
Authors: Strickland R. W. , Webb J. , Richardson F. S. 
Published: December 2004

AbstractThe near ultraviolet chiroptical properties of L‐cystine conformational isomers are examined on a static, “one‐electron” model in which the disulfide moiety is the chromophoric group and the atoms of the L‐alanyl fragments are treated as perturbers. The zeroth order chromophoric wave functions are calculated on a semiempirical molecular orbital model in which excited states are constructed in the virtual orbital‐configuration interaction approximation. The perturbing environment is represented by point charges located at the atomic centers of the L‐alanyl fragments. Chromophore–perturber interactions are expressed as charge–multipole moments with only the charge–dipole and charged–quadrupole terms being retained in the calculations. Vicinal contributions to the rotatory strengths of the five lowest energy disulfide transitions are computed for 30 conformational isomers of the L‐cystine dizwitterion. The results provide support for the view that vicinal or peripheral effects can account entirely for the observed near ultraviolet (λ > 230 nm) chiroptical properties of L‐cystine and its derivatives and that these properties are diagnostic of conformational features external to the disulfide moiety.
A demonstration of two‐component behaviour of the circular dichroic spectra of poly(L‐tyrosine, 3‐bromo‐L‐tyrosine) in trimethylphosphate
Authors: Applequist Jon , Lunde Barbara K. 
Published: December 2004

AbstractThe circular dichroic spectrum of poly(Tyr,TyrBr) in trimethylphosphate from 180 to 320 nm is found to be a linear function of composition from 25 to 68% TyrBr, and the spectra of the Tyr and TyrBr components are resolved. For Tyr the resolved spectrum is in agreement with available CD spectra of poly(Tyr). These results are interpreted to mean that the side‐chain conformations of Tyr and TyrBr are not affected by the other component, and that for Tyr the conformation is the same as in poly(Tyr). It is also concluded that poly(Tyr,TyrBr) is helical with the same helix sense as poly(Tyr). The restrictions on the side‐chain conformations are discussed, and it is suggested that the Tyr and TyrBr side chains are all in the same χ1 region.
Raman spectral changes induced by side‐chain interactions in racemic poly‐γ‐benzyl glutamate
Authors: Wilser Walter T. , Fitchen D. B. 
Published: December 2004

AbstractLaser Raman spectra are reported for solid films cast from a series of solutions containing mixtures of right‐ and left‐handed α‐helices of poly‐γ‐benzyl‐L‐ and D‐glutamate. Procedures were established for producing spectra that were reproducible in position to ±0.3 cm−1 and in relative intensity to a few percent for features of interest. Spectra for the pure L and pure D polymers were identical, as expected. Several small but definite spectral changes appear in the mixtures, reaching a maximum for the racemic 50:50 mixture. The changes are a shift of −1.4 cm−1 in the amide I peak at 1650.5 cm−1; a shift of about −5 cm−1 in the partially resolved amide III peak at 1291 cm−1; a shift of +2.5 cm−1 in the benzyl peak at 3062.5 cm−1; changes in relative intensity of as much as 50% in several regions; and the marked enhancement of several peaks, particularly that at 254 cm−1. These changes are discussed in terms of side‐chain interactions in the packing of right‐ and left‐handed helices.
Stacking specificity and polarization. Comparative synopsis of affinity data
Authors: Lawaczeck Rüdiger , Wagner Karl G. 
Published: December 2004

AbstractAn explanation is given of the specificity of stacking associations based on suggestions of the contribution of dipole‐induced dipole interactions, which emphasize bond moments as the origin of the polarizing power and polarizability of the π‐electron ring system concerned. This explanation is consistent with our own experimental data and with those of other authors on nucleoside self‐association, the mixed interaction of different nucleic acid constituents, and the interaction of aromatic amino acids with nucleosides, nucleotides, and nucleic acids.
Spatial configuration of single‐stranded polynucleotides. Calculations of average dimensions and nmr coupling constants
Authors: Tewari Ravindra , Nanda Rabindra K. , Govil Girjesh 
Published: December 2004

AbstractThe probability distributions of the torsional angles (Φ′, ω′, ω, Φ, and ψ), which fix the structure of nucleotide backbone, have been calculated using the results of energy calculations based on extended Huckel theory (EHT), complete neglect of differential overlap (CNDO), perturbative configuration interaction using localized orbitals (PCILO), and classical potential functions (CPF) methods. Statistical average values of the vicinal 1H1H, 1H31P, and 13C31P nmr coupling constants 〈J〉 have been calculated from the generalized Karplus relations using the probability distribution in the Φ′, Φ, and ψ space. Experimental 〈J〉 values for polyribouridylic acid (polyU) support the theoretical predictions for these torsional angles. Using Monte Carlo technique, random coils of single‐stranded polynucleotides have been simulated and the mean‐square end‐to‐end distance 〈r2〉 has been calculated. Molecular orbital methods (EHT, CNDO, and PCILO) suggest considerable flexibility around OP bonds, leading to fairly small values for the characteristic ratio (C∞ ∼ 4). Observed values of the unperturbed characteristic ratio for polynucleotides are quite large (C∞ ∼ 18) suggesting a relatively rigid nucleotide backbone. The results based on molecular orbital calculations can be reconciled with the experimental values by introducing an additional stabilization of ∼2 kcal mol−1 for the predicted minimum energy ragion (Φ′ ∼ 240°, ω′ ∼ 290°, ω 290°, Φ 180°, and ψ 60°). Such a stabilization may arise from the association of water molecules and metal ions with the phosphate group and (or) Coulomb interaction between neighboring phosphate groups. The calculations provide a semiquantitative estimate of torsional rigidity in the nucleotide backbone.
The influence of alcohol–water solvents on the conformation of deoxyribonucleic acid
Authors: Frisman E. V. , Veselkov A. N. , Slonitsky S. V. , Karavaev L. S. , Vorob'ev V. I. 
Published: December 2004

AbstractThe influence of alcohol–water solvents on the conformation of native DNA was studied by the methods of flow birefrigence and viscometry. Conformational transitions of DNA were observed at low alcohol concentrations corresponding to the destruction of the water spatial structure. A change in the secondary structure of the DNA molecule was observed at high ethanol concentrations and is discussed in the paper.
The stability of RNA hairpin loops containing A–U–G: An–U–G–Um
Authors: Wickstrom Eric , Tinoco Ignacio 
Published: December 2004

AbstractRNA oligomers with the sequence An‐U‐G‐Um, n = 7–9, m = 5–10, have been synthesized and found to form hairpin loops in 21 mM or 101 mM Na+. The hairpin loops displayed melting temperatures 13°–29°C greater than that of the hairpin loop A6‐C8‐U6 in the same solvent. The increased stability of these hairpin loops is attributed to the presence of the trinucleotide A‐U‐G in the loop.Circular dichroism (CD) spectra were taken of the hairpin loops A7‐U‐G‐U6,7,8, A8‐U‐G‐U6,7,8, and A9‐U‐G‐U6 in 21 mM Na+, and compared with circular dichroism spectra of A6‐U6 in 1 M Na+. Difference spectra were calculated between each An‐U‐G‐Um and 11.5 mM (nucleotide) A6‐U6 at similar temperatures and identical singlestrand fractions to give the “experimental” CD spectrum of the unbase‐paired nucleotides in the loop, assuming, five, six, or seven base pairs. CD spectra were calculated for each of the assumed unbase‐paired sequences using the measured CD spectra of ApA, A‐U‐G‐, A, and U, and compared with the experimental spectra. The best agreement was found for hairpin‐loop models containing five base pairs and five to eight unbase‐paired nucleotides in the loop.
Effect of hydration upon the thermal stability of tropocollagen and its dependence on the presence of neutral salts
Authors: Luescher Madeleine , Rüegg M. , Schindler P. 
Published: December 2004

AbstractThe endotherm enthalpy changes ΔHD and temperatures TD of thermal denaturation of tropocollagen fibers were measured by DSC calorimetry as functions of water content. The denaturation temperatures decrease with increasing water content. The enthalpy change values increase sharply in the range 0–28% of water content, where a maximum of 14.3 cal g−1 is reached. The effect of water uptake on the enthalpy term is explained by water bridge formation within the collagen triple helix. Evidence is given for the existence of approximately three intercatenary water bridges per triplet at the enthalpy maximum, their H‐bond energy amounting to approximately 4000 kcal/mol of protein. In the 30–60% range of water content, ΔHD decreases by 2 cal−1 probably due to interactions between secondary water structures and the stabilizing intrahelical water bonds.The influence of two neutral potassium salts, with a structure‐stabilizing and a structure‐breaking anion (F− and I−), on the hydration dependence of ΔHD and TD was also studied. It was shown that the primary hydration is not influenced by these ions, but that TD and ΔHD are altered in an ion specific way in the presence of interface and bulk water. Hydrophobic interactions do not explain the experimental results. A reaction mechanism of the effects of ions upon the structural stability of collagen is proposed and discussed in terms of interactions of the medium water molecules with the intrahelical water bonds, and in terms of proton‐donor/proton‐acceptor equilibria between peptide groups, hydrated ions, and intrahelical water molecules.
Lattice vibrational modes of poly(rU) and poly(rA)
Authors: Eyster James M. , Prohofsky Earl W. 
Published: December 2004

AbstractA normal coordinate analysis has been performed for the polyribonucleotides poly(rU) and poly(rA). The polymers are assumed to be 11‐fold infinite helical structures in the A conformation. The hydrogen atoms have been rigidly attached to the appropriate atoms in order to reduce the dimension of the problem. The potential energy is defined in terms of a valence force field initially and a model for the inclusion of nonbonded interactions has been presented. A method for factoring the secular equation for infinite helical polymers in Cartesian coordinates is presented. All of the general features of polyribonucleotide spectra have been reproduced and, in many cases, good quantitative agreement between observed and calculated frequencies is obtained. More specific assignments are offered for some of the observed lines.
Lattice vibrational modes of poly (rU)·poly(rA). A coupled single‐helical approach
Authors: Eyster James M. , Prohofsky Earl W. 
Published: December 2004

AbstractThe eigenvalues and eigenvectors of 11‐fold double‐helical poly(rU)·poly(rA) have been calculated. The vibrational potential energy of the double‐helical structure is initially considered to be a sum of the vibrational potential energy of the single‐helical structures poly(rU) and poly(rA). Coupling between the single helices is introduced by including a stretch force constant for each hydrogen bond between the uracil and adenine base residues. In addition, a model is presented for nonbonded interactions between nearest neighbor base pairs, which is consistent with a previous model for such interactions in the single helices. Because of the simple structural relationship between the uncoupled single helices and the double helix we are able to cast the secular equation for poly(rU)·poly(rA) in a form suitable for the use of perturbation theory using the previously calculated normal modes for the single helices as the unperturbed modes. Perturbation theory was found to be inapplicable for the region of the spectrum ≲450 cm−1. In this region an exact Green function technique is used to calculate the strongly coupled modes. We explicitly display one aspect of these double‐helical normal modes. The stretching motions of the hydrogen bonds in the region of the spectrum <450 cm−1 have been plotted as bar graphs for each mode.
Melting and premelting phenomenon in DNA by laser Raman scattering
Authors: Erfurth Stephen C. , Peticolas Warner L. 
Published: December 2004

AbstractRaman spectra of DNA from calf thymus DNA have been taken over a wide range of temperatures (25°–95°) in both D2O and H2O. A study of the temperature dependence of the Raman spectra shows that the temperature profiles of the intensities and frequencies of the various bands fall into four different categories: (1) base bands that show a reversible increase in intensity prior to the melting region, i.e., a definite premelting phenomenon; (2) base bands that show little or no temperature dependence; (3) deoxyribose‐phosphate backbone vibrations that show no temperature dependence up to the melting region, at which point large decreases in intensity occur; and (4) slow frequency changes in certain in‐plane vibrations of guanine and adenine due to deuteration of the C‐8 hydrogen of these purines in D2O.Certain Raman bands arising from each of the four bases, adenine, thymine, guanine, and cytosine have been found to undergo a gradual increase in intensity prior to the melting region at which point large, abrupt increases in intensity occur. The carbonyl stretching band of thymine, involved in the interbase hydrogen bonding actually undergoes both a gradual shift to a lower frequency as well as an increase in intensity. These changes provide evidence that some change in the geometry of the bases relative to each other begins to occur around 50°C, well below the melting region of 70°–85°C.From the spectra taken at various temperatures, the DNA appears to remain in the B conformation until the melting point is reached, at which time the DNA progresses into a disordered random‐coil form. No A‐form conformation is found either in the premelting or the melting region.
Conformational studies of poly‐β‐1‐naphthylmethyl‐L‐aspartate
Authors: Ueno Akihiko , Ishiguro Toshio , Toda Fujio , Uno Keikichi , Iwakura Yoshio 
Published: December 2004

AbstractPoly‐β‐1‐naphthylmethyl‐L‐aspartate and copolymers of β‐1‐naphthylmethyl‐L‐aspartate and γ‐benzyl‐L‐glutamate were prepared. From the results obtained by a study of infrared and circular dichroism spectra, poly‐β‐1‐naphthylmethyl‐L‐aspartate was found to be a left‐handed α‐helix both in the solid state and in solution. The fluorescence spectra of these polymers showed excimer emission of the naphthyl chromophores and gave some information about the arrangement of the side‐chain chromophores. By optical titration experiments, it was found that an increasing amount of β‐1‐naphthylmethyl‐L‐aspartate residues in the copolymers induces a progressive instability of the helical structure.
Electric birefringence studies on polyglutamic acid
Authors: Kobayasi Syoyu , Ikegami Akira 
Published: December 2004

AbstractThe electric birefringence for the aqueous solution of poly‐L‐glutamic acid (PGA) in the helical form was studied. PGA samples were fractionated by gel column chromatography. PGA showed a positive electric birefringence. The permanent dipole moment of the PGA molecule was suggested to be largely suppressed. The measurements of the intrinsic Kerr constants for various molecular lengths showed that the electric anisotropy (polarizability) of PGA is proportional to the 1.5 power of the length. The electric birefrigence measurement was also carried out in the helix–coil transition region. The Kerr constant of PGA was largely reduced on going from the helical form to the coiled form.
The precipitation of poly‐L‐glutamic acid. II. β‐Precipitation
Authors: Zimmerman S. S. , Clark J. C. , Mandelkern L. 
Published: December 2004

AbstractInfrared and X‐ray diffraction studies have established that in the β‐precipitation region of poly‐L‐glutamic acid the chains are in the β‐conformation. Therefore, a major molecular conformational change has taken place upon precipitation. It is shown that the size of the α‐helical aggregates remains constant with time in the β‐region. Strong evidence can be offered to indicate that the transformation involves a transitory random‐coil intermediate. Reasons are advanced, in view of the stability of the β‐form, as to why two distinct precipitation regions exist.