bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rotational dynamics of DNA from 10−10 to 10−5 seconds: Comparison of theory with optical experiments
Authors: Shibata John H. , Fujimoto Bryant S. , Schurr J. Michael 
Published: May 2005

AbstractOptical anisotropy data spanning a very wide time range are analyzed using a recently developed theory for filamentous macromolecules that can bend, twist, and also admit overdamped local libration (or wobble) of the chromophore. A rapid relaxation in the fluorescence polarization anisotropy (FPA) near 10−10 s is fitted well by superimposing isotropic wobble of the chromophore (7° rms polar and azimuthal amplitude) on the long‐wavelength twisting and bending motions that characterize the relaxation at longer times but not by the latter alone. Moreover, the decay of the FPA from 0.5 to 150 ns cannot be satisfactorily fitted by chromophore wobble in an otherwise rigid DNA and must be assigned primarily to twisting, as noted previously.Data from 26 ns to 20 μs for 600 base‐pair DNA are accurately fitted with only a single adjustable scaling factor when the tumbling correlation function is taken to be the empirical electric birefringence decay function of Elias and Eden. The Barkley‐Zimm (BZ) tumbling correlation for very long filaments appears to decay too rapidly and results in significant overestimation of the depolarization for t ≤ 300 ns. In the range of the FPA experiments (t ≥ 150 ns), equally good fits with equally uniform torsion constants are obtained for long DNAs, whether one assumes the BZ tumbling correlation function or neglects tumbling entirely, but the best‐fit torsion constant (actually the product of the torsion constant and friction factor) is increased by the factor 1.9 when the BZ result is used with a persistence length of a = 500 Å. The BZ bending theory is compared with other experimental data, and also with a simulation at very short times with mixed results. Present uncertainties regarding the tumbling dynamics and the friction factor for azimuthal rotation allow the torsion constant to be as much as 3.8 times larger than the initial estimate of Thomas et al. Apparent torsion constants obtained from relative ligase kinetics measurements are also briefly discussed.
Conformational studies on the bacterial cell wall peptide analog phenylacetyl‐D‐alanyl‐D‐alanine: Comparison between conformations of cell wall peptide analog and those of penicillin G
Authors: Labischinski H. , Barnickel G. , Naumann D. , Rönspeck W. , Bradaczek H. 
Published: May 2005

AbstractThe conformation of phenylacetyl‐D‐alanyl‐D‐alanine in the crystalline state was characterized by Fourier‐transform ir and Raman spectroscopy and was unambiguously solved by x‐ray single‐crystal determination. In the crystalline state, the molecule adopts a partially folded conformation quite similar to that of another cell wall peptide, acetyl‐D‐alanyl‐D‐alanine [Benedetti et al. (1981) J. Biol. Chem. 256, 9229–9234], although the crystal structure is stabilized by a quite different intermolecular hydrogen‐bond pattern. No significant deviation from the usual trans‐planar peptide group geometry was detected. The conformations accessible in the noncrystalline state were investigated by ir measurements in solution and conformational energy calculations. The theoretical study revealed that the peptide is a highly flexible molecule, since 55 minima were detected, within 3 kcal/mol, including the conformation found in the single crystal. The ir data for phenylacetyl‐D‐alanyl‐D‐alanine in different solvents were in accordance with virtually extended conformations, with some indication for weak, intramolecularly hydrogen‐bonded C5‐rings. These conformational data obtained for the cell wall peptide analog are compared with those known for penicillin G in the crystalline state.
Concentration dependence of proteoglycan diffusion
Authors: Harper Gregory S. , Comper Wayne D. , Preston Barry N. , Daivis Peter 
Published: May 2005

AbstractThe mutual diffusion coefficient of the bovine nasal cartilage proteoglycan subunit is found to increase rapidly with increasing concentration and decreasing ionic strength. These results have been obtained by analysis of the boundary relaxation of concentration gradients in the analytical ultracentrifuge by schlieren optics. The diffusion behavior can be understood in terms of the nonideality of the proteoglycan. The magnitude of the nonideality is dominated by charge interactions, whereas the influence of molecular size and associated excluded‐volume interactions is small. The concentration dependence of the apparent diffusion coefficient of the proteoglycan subunit from dynamic light scattering was found, in contrast, to decrease with increasing concentration. Computer simulation of the dynamic light scattering suggests that the presence of a small population of aggregates may account for the difference in the two types of diffusion measurement due to their marked influence on the scattering.
Enthalpies of transfer for proteins from aqueous to water‐alcohol solutions: A test for models of residues exposed to solvent
Authors: Schrier M. Y. , Defoster G. , Schrier E. E. , Starzak M. 
Published: May 2005

AbstractThe enthalpies of transfer of proteins from aqueous solution to alcohol–water solutions are used as probes of solvent‐accessible surface for these proteins. Enthalpies of transfer to 10 wt% ethanol solutions are determined calorimetrically for the native proteins ribonuclease A, lysozyme, and ovalbumin. Ribonuclease A and lysozyme are reduced and carboxamidomethylated to produce configurations in which interior residues of the native protein are exposed to the solvent; enthalpies of transfer are determined for these species. These data are then compared with enthalpies of transfer for the constituent amino acids of the proteins. The enthalpies of transfer for the residues are used to generate a maximal enthalpy of transfer that can be compared with the enthalpies of transfer for the reduced, carboxamidomethylated proteins. The residue amino acid enthalpies are coupled with probabilities that each residue is an exterior residue to predict an enthalpy of transfer for the native protein that can be compared with the observed enthalpy. The probabilities developed by Wertz and Scheraga and Lee and Richards, and Chothia are then compared on their ability to predict the native enthalpies of transfer for the protein. The Wertz–Scheraga model gives the better fit of this data in all cases.
Crowned dopa's, their dimers, cyclodimers and polymers: Synthesis and cation complexation
Authors: Berthet Michele , Sonveaux Etienne 
Published: May 2005

AbstractOptically pure protected L‐[3,4‐(1,4,7,10,13‐pentaoxatridecamethylene) phenyl] alanine, its dipeptide, diketopiperazine and homopolymer, protected L‐[3,4‐(1,4,7,10,13,16‐hexaoxahexadecamethylene) phenyl] alanine and its polymer have been synthesized and characterized. These crown ether derivatives complex the potassium and ammonium cations as well as protonated leucine and glycine in tetrahydrofuran and methanol. They are also phase‐transfer agents. The cooperativity of the crown units was studied in detail for the dimeric ligands.
Determination of thermodynamic functions from scanning calorimetry data
Authors: Kidokoro Shun‐Ichi , Wada Akiyoshi 
Published: May 2005

AbstractWe present a theoretical basis and new methods for the determination of thermodynamic functions from scanning calorimetry data. A thermodynamic state is defined here as an ensemble of microstates in the system, and it can be defined only through assumptions of its heat capacity function and the two integral constants. With these assumptions, scanning calorimetry data can be analyzed using the single or double (or multi‐) deconvolution presented here. New equations to calculate the van't Hoff enthalpy function and the calorimetric enthalpy function are presented. We prove that the agreement of these two functions is a necessary and sufficient factor for the condition that the system can be described with the assumed two‐state model.
Loop formation in polynucleotide chains. II. Flexibility of the anticodon loop of tRNAPhe
Authors: Marky Nancy L. , Olson Wilma K. 
Published: May 2005

AbstractThe flexibility of hairpin loops containing n bases (residues) has been examined using a theoretical model [N. L. Marky and W. K. Olson (1982), Biopolymers, 21, 2329–2344] of oligonucleotide loop closure. The study is based on correlated probabilities of chain separation and terminal residue orientation as outlined previously. The probabilities are calculated using standard statistical mechanical methods as functions of local conformational changes of the chain backbone. Our results for an RNA chain of 9 residues suggest that the anticodon loop is a dynamic structure capable of assuming a variety of different spatial conformations. Free energy values related to the various conformations span a narrow range of values (2–4 kcal/mole) and compare well with experimental observations in aqueous solution. Conformational transitions between the loop conformations are within less than 0.5 kcal/mole in free energy. The different spatial loop conformations and the likely pathways between them may have potential relevance to the molecular translation of the genetic code.
The optical properties of Li‐ and Na‐DNA films
Authors: Weidlich T. , Lindsay S. M. , Rupprecht A. 
Published: May 2005

AbstractWe have measured the refractive indices of highly crystalline Li‐ and Na‐DNA wet‐spun films as a function of their water content using an immersion technique. We calculated the molecular polarizabilities of a DNA base pair using the Lorentz–Lorenz relation for anisotropic materials, the measured water contents, and densities corrected for void formation. For Li‐DNA, the polarizabilities are independent of the relative humidity, whereas for Na‐DNA, there are large changes at the A‐B transition and also at low humidities. The average polarizability of A‐Na‐DNA is in agreement with that calculated from refractive index increments and also as calculated by a simple addition of bond polarizabilities, whereas the values for Li‐ and B‐Na‐DNA are about 30% larger than the calculated values. We propose that these anomalous values are due to nonlinear polarizabilities of the phosphate group.
Conformation of the oligonucleotide d(AAAAAATTTTTT)2 by two‐dimensional nuclear overhauser effect spectroscopy and its relevance to poly(dA) · poly(dT)
Authors: Roy Siddhartha , Borah Babul , Zon Gerald , Cohen Jack S. 
Published: May 2005

AbstractConformational analysis from the pattern and intensities of cross‐peaks in the two‐dimensional nuclear Overhauser effect proton nmr spectra of the homopolymer, poly(dA) · poly(dT), and the analogous oligomer, d(AAAAAATTTTTT)2, indicate that they both exist in the B‐conformation. The conformation of the ApT/TpA junction in the oligomer is significantly different from the rest of the base pairs.
A proton NMR spin‐lattice relaxation study of the imino proton exchange kinetics in calf‐thymus DNA
Authors: Bendel Peter 
Published: May 2005

AbstractThe results of semiselective 1H‐nmr inversion recovery experiments on sonicated calf thymus DNA fragments are reported. The measurements were conducted in aqueous solutions containing 85% D2O, in order to reduce the dipolar contribution to the observed relaxation rates. In solutions containing 0.2M NaCl, 0.4 mM EDTA, and 10 mM cacodylate at pH = 7.0, the exchange rates of the imino protons in A‐T base pairs confirm values published earlier in the literature, extrapolating to 0.25 s−1 at 25°C. Corresponding values for the G‐C base pairs are published for the first time, and are about sixfold slower. The addition of up to 0.1M Tris buffer (pH = 7.3 at 25°C), caused a striking increase in the measured exchange rates for both the A‐T and G‐C imino protons, resembling the effect recently observed for poly(rA)‐poly(rU) and poly(rI)‐poly(rC), and suggesting that the exchange rates measured for nucleic acid duplexes in low buffer concentrations at neutral pH do not reflect base‐pair opening rates as assumed in the past. Lower limits to the base‐pair opening rates could be estimated from extrapolation of the experimental data to infinite buffer concentration, and are 1 × 103 s−1 for the A‐T, and 50 s−1 for the G‐C, base paris at 62°C.
The hydrogen bonding of cytosine with guanine: Calorimetric and 1H‐NMR analysis of the molecular interactions of nucleic acid bases
Authors: Williams Loren Dean , Chawla B. , Shaw Barbara Ramsay 
Published: May 2005

AbstractThe enthalpy of hydrogen‐bond formation between guanine (G) and cytosine (C) in o‐dichlorobenzene and in chloroform at 25°C has been determined by direct calorimetric measurement. We derivatized 2′‐deoxyguanosine and 2′‐deoxycytidine at the 5′‐ and 3′‐hydroxyls with triisopropylsilyl groups; these groups increase the solubility of the nucleic acid bases in nonaqueous solvents. Such derivatization also prevents the ribose hydroxyls from forming hydrogen bonds. Consequently, hydrogen‐bond formation in our system is primarily between the bases, and to a lesser extent, between base and solvent, and can be measured directly with calorimetry. To obtain the data on base‐pair formation, we first took into account the contributions from self‐association of each base, and where possible, have determined the ΔH of self‐association. From isoperibolic titration calorimetry, our measured ΔH of C2 formation in chloroform is −1.7 kcal/mol of C. Our measured ΔH of C:G base‐pair formation in o‐dichlorobenzene is −6.65 ± 0.32 kcal/mol. Since o‐dichlorobenzene does not form hydrogen bonds, the ΔH of C:G base‐pair formation in this solvent represents the ΔH of the hydrogen‐bonding interaction of C with G in a nonassociating solvent. In contrast, our measured ΔH of C:G base‐pair formation in chloroform is −5.77 ± 0.20 kcal/mol; thus, the absolute value of the enthalpy of hydrogen bonding in the C:G base pair is greater in o‐dichlorobenzene than in chloroform. Since chloroform is a solvent known to form hydrogen bonds, the decrease in enthalpic contribution to C:G base pairing in chloroform is due to the formation of hydrogen bonds between the bases and the solvent. The ΔH of hydrogen bonding of G with C reported here differs from previous indirect estimates: Our measurements indicate the ΔH is 50% less in magnitude than the ΔH based on spectroscopic measurements of the extent of interaction. We have also observed that the enthalpy of hydrogen bonding of C with G in chloroform is greater when G is in excess than when C is in excess. This increased heat is due to the formation of C:Gn > 1 complexes that we have observed using 1H‐nmr. Although C:G2 structures have previously been observed in triple‐stranded polymeric nucleic acids, higher order structures have not been observed between C and G monomers in nonaqueous solvents until now. By using monomers as a model system to investigate hydrogen‐bonding interactions in DNA and RNA, we have obtained the following results: A direct measurement of the ΔH of hydrogen bonding in the C:G complex in two nonaqueous solvents, and the first observation of C:Gn > 1 complexes between monomers. These results reinforce the importance of hydrogen bonding in the stabilization of various nucleic acid secondary and tertiary structures.
Stability of polypeptide conformational states as determined by computer simulation of the free energy
Authors: Meirovitch H. , Vásquez M. , Scheraga H. A. 
Published: May 2005

AbstractA method is developed to extract the entropy of polypeptides and proteins from samples of conformations. It is based on techniques suggested previously by Meirovitch, and has the advantage that it can be applied not only to states in which the molecule undergoes harmonic or quasiharmonic conformational fluctuations, but also to the random coil, as well as to mixtures of these extreme states. In order to confine the search to a region of conformational space corresponding to a stable state, the transition probabilities are determined not by “looking to the future,” as in the previous method [H. Meirovitch and H. A. Scheraga (1986) J. Chem. Phys. 84, 6369–6375], but by analyzing the previous steps in the generation of the chain. The method is applied to a model of decaglycine with rigid geometry, using the potential energy function ECEPP (Empirical Conformational Energy Program for Peptides). The model is simulated with the Metropolis Monte Carlo method to generate samples of conformations in the α‐helical and hairpin regions, respectively, at T = 100 K. For the α‐helix, the four dihedral angles of the N‐ and C‐terminal residues are found to undergo full rotational variation. The results show that the α‐helix is a more stable structure than the hairpin. Both its Helmholtz free energy F and energy E are lower than those of the hairpin by ΔF ∼ 0.4 and ΔE ∼ 0.3 kcal/mole/residue, respectively. It should be noted that the contribution of the entropy ΔS to ΔF is significant (TΔS ∼ 0.1 kcal/mole/residue). Also, the entropy of the α‐helix is found to be larger than that of the hairpin. This is a result of the extra entropy arising from the rotational freedom about the four terminal single bonds of the α‐helix.
Structural determinants of spermidine–DNA interactions
Authors: Vertino Paula M. , Bergeron R. J. , Cavanaugh Paul F. , Porter Carl W. 
Published: May 2005

AbstractTwelve different analogs of spermidine (SPD) and SPD itself were compared for their ability to modulate two conformational transitions of DNA; the B‐to‐Z conformational transition of poly(dG‐me5dC) and the thermal melting transition of calf thymus DNA. The analogs consisted of five N‐ethyl‐SPD derivatives [N1‐ethyl‐SPD, N4‐ethyl‐SPD, N8‐ethyl‐SPD, N1,N8‐bis(ethyl)SPD and N1,N4,N8‐tri(ethyl)SPD], which differed in the number and/or position of the ethyl substitution (the alkyl series); three N‐acetyl‐SPD derivatives (N1‐acetyl‐SPD, N4‐acetyl‐SPD, and N8‐acetyl‐SPD), which were comparable to the N‐ethyl‐SPD derivatives but not protonated at the substituted amine (the acyl series); three aliphatic analogs [nor‐SPD, homo‐SPD, and N1,N9‐bis(ethyl)homo‐SPD], which differed in the interamine carbon chain length (homolog series), and 1,8‐diaminooctane, which was comparable in overall chain length to SPD but lacked a central nitrogen. By comparing the relative abilities of the various analogs and SPD to modulate DNA structural transitions, it is possible to gain insight into the relative significance of the number and location of protonated amines (acyl series), the number and location of steric groups (alkyl series), aliphatic chain length (homolog series), and the central amine (1,8‐diaminooctane) as determinants of SPD–DNA interactions. The B‐to‐Z conformational transition was facilitated to a midpoint by 2.4 μM SPD under conditions of low (i.e., 11 mM Na+) ionic strength. The phenomenon was affected most significantly by the number of protonated amines followed in rank order by location of the protonated amines, number of steric groups (bulk), steric group location, and aliphatic chain length. Stabilization of DNA to thermal melting was also most affected by the number of protonated amines followed by aliphatic chain length, number of steric groups, and location of protonated amines. In general, substitutions at the central (N4) amine of SPD exerted a significant influence on the B‐to‐Z transition but not on thermal melting.
Gas‐phase IR spectra of substituted alkylamides
Authors: Venkatachalapathi Yalamoori V. , Mierke Dale F. , Taulane Joseph P. , Goodman Murray 
Published: May 2005

AbstractThe source of the splittings observed in the amide A, I, II, and III absorption bands of N‐methylacetamide (NMA) have been determined by high‐resolution gas‐phase FTIR. Analysis of isotopically labeled NMA, along with simpler amides (formamide, acetamide) show that the observed splitting arise from rotational transitions within the vibrational manifold. The ir spectra of a homologous series of monosubstituted alkylamides are also examined. The observed effects on the ir spectra from incorporating substituents from methyl to t‐butyl on both sides of the amide linkage are discussed in terms of rotational transitions and coupled oscillations. During these studies we did not observe any evidence for the presence of cis conformations of the amide bond.
Bisintercalation of ditercalinium into a d[CpGpCpG]2 minihelix: Structure and dynamics aspects—a 400‐MHz 1H‐nmr study
Authors: Delbarre A. , Delepierre M. , D'Estaintot B. Langlois , Igolen J. , Roques B. P. 
Published: May 2005

AbstractThe structure of the complex formed in aqueous solution at pH 5.5 between ditercalinium, a potent antitumoral 7H‐pyrido[4,3‐c]carbazole rigid dimer, and the self‐complementary tetranucleotide d[CpGpCpG], was investigated by 400‐MHz 1H‐nmr. For a 1:2.5 drug‐to‐helix ratio, the dimer was only found in bound form, whereas free and complexed tetranucleotide were in slow exchange. This allowed unambiguous assignment of the protons in the complex through exchange polarization transfer measurements. The tetranucleotide existed as a right‐handed double helix in the complex. The strong upfield shifts measured on most aromatic protons on both drug and nucleobases as well as on DNA imino protons were consistent with bisintercalation of the dimer. According to the negative nuclear Overhauser effects generated to protons on the convex edge of the bound drug rings by saturation of sugar protons, it was concluded that ditercalinium was intercalated with its rigid bis‐ethyl bispiperidine spacer fitting the major groove of the helix. Difference in antitumor activity of various pyridocarbazole dimers is discussed in relation to the binding kinetics and the complex geometry determined in this study.
A 43Ca‐nmr study of Ca(II)–DNA interactions
Authors: Braunlin William H. , Drakenberg Torbjörn , Nordenskiöld Lars 
Published: May 2005

AbstractHigh‐field 43Ca‐nmr is applied to characterize the interactions of calcium ions with double‐helical DNA. Under the conditions examined, 43Ca lineshapes are always Lorentzian and single spin‐lattice relaxation rates are obtained. The measured transverse and longitudinal relaxation rates are, however, not equal, which implies that the relaxation is in the near‐extreme narrowing regime. Relative to the transverse relaxation rate, calcium ions near the DNA exchange rapidly with the bulk solution. The 43Ca linewidths, spin‐lattice relaxation rates, and chemical shifts observed over the course of a titration of DNA with calcium salt are not well described by simple electrostatic models. Deviations are most pronounced at low ratios of calcium to DNA phosphate. In contrast, at higher Ca/P ratios, the changes observed are well described by an electrostatic model based on the Poisson–Boltzmann equation. These results suggest that there is a small class of site‐bound calcium as well as a large background of delocalized calcium electrostatically associated with the DNA. In contrast to previous studies of 25Mg2+–DNA interactions, for which significant site‐binding effects were also indicated, it appears rather easy to displace bound 43Ca2+ by competition with sodium or magnesium cations. Unfortunately, neither these earlier results nor the present work allows a precise quantitation of the extent of site‐bound divalent cation.