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  • Polymer and Materials Science  (30)
  • Theoretical, Physical and Computational Chemistry  (5)
  • 1
    Digitale Medien
    Digitale Medien
    Interaction of the antimalarial drug fluoroquine with DNA, tRNA, and poly(A): 19F-NMR chemical-shift and relaxation, optical absorption, and fluorescence studies (1981)
    New York : Wiley-Blackwell
    Biopolymers 20 (1981), S. 435-449 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The interaction of the fluorinated antimalarial drug fluoroquine [7-fluoro-4-(diethyl-amino-1-methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F-nmr chemical-shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well-known analog chloroquine. At low drug-to-base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F-nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F-nmr relaxation experiments were carried out to measure the spin-lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off-resonance intensity ratio (R), off-resonance rotating-frame spin-lattice relaxation time (T1ρoff), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton-fluorine dipolar and chemical-shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine-DNA complex can be well described by a motional model incorporating long-range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.1981.360200303
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  • 2
    Digitale Medien
    Digitale Medien
    Molecular mechanical studies on left- and right-handed B-DNA (1987)
    New York : Wiley-Blackwell
    Biopolymers 26 (1987), S. 403-414 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Molecular mechanical simulations on base-paired deoxyhexanucleoside phosphates, (dAdT)3 · (dAdT)3, (dTdA)3 · (dTdA)3, (dGdC)3 · (dGdC)3, and (dCdG)3 · (dCdG)3, have been carried out to assess their energetic stabilities in left- and right-handed forms. These hexamers have also been simulated with alternating sugar-puckering profiles with the combinations (purine : C2′-endo-pyrimidine : C3′-endo) and (purine : C3′-endo-pyrimidine C2′-endo). The right-handed models have been found to be the energetically most stable structures and the left-handed structures are significantly destabilized. This instability has been rationalized in terms of competition between stabilizing stacking interactions on one hand, and distortions in the bond angles and torsion angles in the sugar-phosphate backbone on the other.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360260308
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  • 3
    Digitale Medien
    Digitale Medien
    Effects of nucleotide bromination on the stabilities of Z-RNA and Z-DNA: A molecular mechanics/thermodynamic perturbation study (1989)
    New York : Wiley-Blackwell
    Biopolymers 28 (1989), S. 1939-1957 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: The structures of ZI- and ZII- form RNA and DNA oligonucleotides were energy minimized in vacuum using the AMBER molecular mechanics force field. Alternating C-G sequences were studied containing either unmodified nucleotides, 8-bromoguanosine in place of all guanosine residues, 5-bromocytidine in place of all cytidine residues, or all modified residues. Some molecules were also energy minimized in the presence of H2O and cations. Free energy perturbation calculations were done in which G8 and C5 hydrogen atoms in one or two residues of Z-form RNAs and DNAs were replaced in a stepwise manner by bromines. Bromination had little effect on the structures of the energy-minimized molecules. Both the minimized molecular energies and the results of the perturbation calculations indicate that bromination of guanosine at C8 will stabilize the Z forms of RNA and DNA relative to the nonbrominated Z form, while bromination of cytidine at C5 stabilizes Z-DNA and destabilizes Z-RNA. These results are in agreement with experimental data. The destabilizing effect of br5C in Z-RNAs is apparently due to an unfavorable interaction between the negatively charged C5 bromine atom and the guanosine hydroxyl group. The vacuum-minimized energies of the ZII- form oligonucleotides are lower than those of the corresponding ZI- form molecules for both RNA and DNA. Previous x-ray diffraction, nmr, and molecular mechanics studies indicate that hydration effects may favor the ZI- conformation over the ZII- form in DNA. Molecular mechanics calculations show that the ZII-ZI energy differences for the RNAs are greater than three times those obtained for the DNAs. This is due to structurally reinforcing hydrogen-bonding interactions involving the hydroxyl groups in the ZII form, especially between the guanosine hydroxyl hydrogen atom and the 3′-adjacent phosphate oxygen. In addition, the cytidine hydroxyl oxygen forms a hydrogen bond with the 5′-adjacent guanosine amino group in the ZII- form molecule. Both of these interactions are less likely in the ZI- form molecule: the former due to the orientation of the GpC phosphate away from the guanosine ribose in the ZI form, and the latter apparently due to competitive hydrogen bonding of the cytidine 2′-hydroxyl hydrogen with the cytosine carbonyl oxygen in the ZI form. The hydrogen-bonding interaction between the cytidine hydroxyl oxygen and the 5′-adjacent guanosine amino group in Z-RNA twists the amino group out of the plane of the base. This may be responsible for differences in the CD and Raman spectra of Z-RNA and Z-DNA.
    Zusätzliches Material: 4 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360281111
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  • 4
    Digitale Medien
    Digitale Medien
    An analysis of the sequence dependence of the structure and energy of A- and B-DNA models using molecular mechannics (1983)
    New York : Wiley-Blackwell
    Biopolymers 22 (1983), S. 969-1002 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: Molecular-mechanics calculations have been carried out on the base-paired hexanucleoside pentaphosphates d(TATATA)2, d(ATATAT)2, d(A6)·d(T6), d(CGCGCG)2, d(GCGCGC)2, and d(C6)·d(G6) in both A- and B-DNA geometries. The calculated relative energies of these polymers are consistent with the relative stabilities of the polymers found experimentally. In particular, the results of our calculations support the observation that the homopolymer d(A)n·d(T)n is more stable in a B-DNA conformation, while the homopolymer d(G)n·d(C)n is more stable in an A-DNA conformation. The molecular interactions responsible for these differential stabilities include both inter- and intrastrand base stacking, as well as base-phosphate interactions. While definitive experiments on the heteropolymer stabilities have not yet been carried out, the results of our calculations also suggest a greater stability of the purine-3′,5′-pyrimidine sequence over the pyrimidine-3′,5′-purine sequence in both the A- and B-conformations. The reason for this greater stability lies in the importance of the inherent directionality (5′ → 3′ vs 3′ → 5′) of phosphate-base and base-base interactions. The largest conformation change observed on energy refinement is sugar repuckering, which occurs mainly on pyrimidine-attched sugars and only in the B-DNA geometry. We suggest a molecular mechanism, specifically, differential base-sugar steric interactions involving neighboring sugars, to explain why this repuckering occurs more with d(A6)·d(T6) than with other isomers.
    Zusätzliches Material: 10 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360220316
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  • 5
    Digitale Medien
    Digitale Medien
    Sequence and conformational effects on imino proton exchange in A · T- and A · U-containing DNA and RNA duplexes (1985)
    New York : Wiley-Blackwell
    Biopolymers 24 (1985), S. 711-724 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: 1H-nmr relaxation has been used to study the effect of sequence and conformation on imino proton exchange in adenine-thymine (A · T) and adenine-uracil (A · U) containing DNA and RNA duplexes. At low temperature, relaxation is caused by dipolar interactions between the imino and the adenine amino and AH2 protons, and at higher temperature, by exchange with the solvent protons. Although room temperature exchange rates vary between 3 and 12s-1, the exchange activation energies (Eα) are insensitive to changes in the duplex sequence (alternating vs homopolymer duplexes), the conformation (B-form DNA vs A-form RNA), and the identity of the pyrimidine base (thymine vs uracil). The average value of the activation energy for the five duplexes studied, poly[d(A-T)], poly[d(A) · d(T)], poly[d(A-U)], Poly[d(A) · d(U)], and poly[r(A) · r(U)], was 16.8 ± 1.3 kcal/mol. In addition, we find that the average Eα for the A.T base pairs in a 43-base-pair restriction fragment is 16.4 ± 1.0 kcal/mol. This result is to be contrasted with the observation that the Eα of cytosine-containing duplexes depends on the sequence, conformation, and substituent groups on the purine and pyrimidine bases. Taken together, the data indicate that there is a common low-energy pathway for the escape of the thymine (uracil) imino protons from the double helix. The absolute values of the exchange rates in the simple sequence polymers are typically 3-10 times faster than in DNAs containing both A · T and G · C base pairs.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360240410
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  • 6
    Digitale Medien
    Digitale Medien
    The calculated free energy effects of 5-methyl cytosine on the B to Z transition in DNA (1990)
    New York : Wiley-Blackwell
    Biopolymers 29 (1990), S. 1193-1209 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: We have examined the free energy effects of 5-methylation of cytosine on the B ↔ Z conformational equilibrium in DNA. Free energy differences were calculated using the free energy perturbation approach, which uses an easily derived equation from classical statistical mechanics to relate the free energy difference between two states to the ensemble average of the potential energy difference between the states. Calculations were carried both in explicit solvent and (for comparison) in vacuo. The free energy values obtained for the explicit solvent systems are total free energies, with contributions from all parts of the system (solvent + solute), and so are relevant to the B ↔ Z transitions observed under real(physiological) conditions. We calculate that in solution, methylation makes the B → Z transition more favorable by about -0.4 kcal/mole base pair (bp) in free energy. This value compares well with approximate experimentally derived values of about -0.3 kcal/ mole-bp. We also discuss a method for determining the free energy difference between conformational states poorly maintained by a potential energy model. Finally, the effects of methylation on the melting temperature of DNA are examined.
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360290810
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  • 7
    Digitale Medien
    Digitale Medien
    A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1115-1134 
    Details
    ISSN: 0006-3525
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie
    Notizen: An understanding of helix dynamics can aid in interpreting the motions of proteins. The conformational transitions that occur also appear to play a role in protein folding. Structural studies of isolated peptides in solution are just becoming available. However, detailed analysis of the helix-coil transition is still not available and will be difficult to obtain experimentally. For these reasons, we performed a long molecular dynamics simulation of polyalanine at high temperature. Using this approach, we obtain a description of the overall structure and inherent flexibility of the chain as well as a structural picture of the conformational changes that occur. In this way, we can address both equilibrium properties of the peptide and the dynamics and mechanism of the structural transitions. Our results correlate fairly well with the available experimental data and previous simulations aimed at addressing α-helix dynamics. The peptide spends the bulk of its time fluctuating between different conformations with intermediate helix contents. Transitions between highly ordered and highly disordered structures were rare, but they occurred rapidly. Our distribution of conformations favored collapsed states. Hence, our transitions to structures with high helical content were from fluctuating compact structures. The conversion between helix and coil occurred sequentially on a residue-by-residue basis. However, there was local cooperativity; the transition of a residue to the coil state was facilitated after a neighboring group became non-helical. The relevance of our results to protein folding is also discussed.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/bip.360310911
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  • 8
    Digitale Medien
    Digitale Medien
    Synthesis and characterisation of poly(arylene sulfide)s, 5Part 4: cf. A. B. Port, R. H. Still, Polymer Deg. Stabil. 2, 1 (1980).. Model compound studies of debromination reactions which occur during the synthesis of poly(arylene sulfide)s from copper(I) 4-bromobenzenethiolates [copper(I) 4-bromothiophenoxides] (1987)
    New York : Wiley-Blackwell
    Die Makromolekulare Chemie 188 (1987), S. 111-118 
    Details
    ISSN: 0025-116X
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Physik
    Notizen: Debromination side-reactions which occur during the synthesis of poly(arylene sulfide)s from copper(I) 4-bromothiophenoxidesSystematic name: Copper(I) 4-bromobenzenethiolates. were investigated using bromobenzene as a model for the end unit in a poly(1,4-phenylene sulfide) chain. Model reactions were conducted in quinoline, pyridine, and 10:1 (v/v) quinoline/pyridine solution in the presence and absence of copper(I) bromide, the condensation product of polymerisation. Reaction liquors were subjected to GLC and MS analysis and evidence is presented which indicates that a copper(I) initiated debromination reaction occurs yielding monophenylquinolines. A mechanism is proposed for the reaction and critically discussed. The consequences of the reaction at the macromolecular level are also described.
    Zusätzliches Material: 2 Tab.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/macp.1987.021880110
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  • 9
    Digitale Medien
    Digitale Medien
    Synthesis and characterisation of poly(arylene sulfides), 6Part 5: cf.16. Synthesis of block copoly(arylene sulfides) (1987)
    New York : Wiley-Blackwell
    Die Makromolekulare Chemie 188 (1987), S. 1537-1549 
    Details
    ISSN: 0025-116X
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Physik
    Notizen: Novel ABA block copolymers of poly(1,4-phenylene sulfide) (PPS(A)) and poly-(2-methyl-1,4-phenylene sulfide) (PMPS(B)) were synthesised from bis(4-bromophenyl) sulfone (BBS) by sequential reaction with copper(I) 4-bromo-2-methylbenzenethiolate (CBMT) and copper(I) 4-bromobenzenethiolate (CBT). PPS, PMPS and PPS/PMPS random copolymers were also prepared to aid block copolymer characterisation. Polymer fractions were studied by hot-stage microscopy to evaluate melting ranges, and molar masses were computed from bromine end-group concentrations and from gel permeation chromatography studies. Compositional analyses were made by IR and 1H NMR spectroscopy leading to confirmation of the block copolymer structure and to evaluation of the degrees of polymerisation of the individual blocks.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/macp.1987.021880701
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  • 10
    Digitale Medien
    Digitale Medien
    Synthesis and characterisation of poly(arylene sulfides), 7Part 6: cf.1. Transitional behavior of random and block copoly(arylene sulfides) (1987)
    New York : Wiley-Blackwell
    Die Makromolekulare Chemie 188 (1987), S. 1551-1560 
    Details
    ISSN: 0025-116X
    Schlagwort(e): Chemistry ; Polymer and Materials Science
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Physik
    Notizen: Differential scanning calorimetry was used to evaluate first and second order transition temperatures and % crystallinity of poly(1,4-phenylene sulfide) (PPS), poly(2-methyl-1,4-phenylene sulfide) (PMPS), their blends and random and block copolymers comprising thio-1,4-phenylene and thio-2-methyl-1,4-phenylene units. Results are discussed in terms of the miscibility of PPS and PMPS in the melt phase and disruption of the crystallisation of PPS units by PMPS units. Microphase separation in the block copolymers was shown to be dominated by crystallisation of the PPS blocks. The application of Krause's microphase separation theory to prediction of the transitional behaviour of the block copolymers is critically discussed.
    Zusätzliches Material: 1 Ill.
    Materialart: Digitale Medien
    URL: http://dx.doi.org/10.1002/macp.1987.021880702
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