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  • 1
    Electronic Resource
    Electronic Resource
    A semiempirical extension of polyelectrolyte theory to the treatment of oligoelectrolytes: Application to oligonucleotide helix-coil transitions (1978)
    New York : Wiley-Blackwell
    Biopolymers 17 (1978), S. 159-166 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The interaction of counterions with a suitably long, charged oligomer appears susceptible to treatment in the context of polyelectrolyte theory by the introduction of an end-effect parameter that reflects the reduced association of counterions with the terminal regions of the oligo-ion. Use of a physically reasonable value for the end-effect parameter provides excellent agreement between theory and the experimental data of Elson, Scheffler, and Baldwin [J. Mol. Biol. 54, 401-415 (1970)] on the dependences of melting temperature on salt concentration and chain length for a series of hairpin helices formed by d(TA) oligomers. The differences in behavior expected for hairpin, dimer, and oligomer-polymer helices are discussed. The salt dependence of the end-joining equilibrium investigated for λ DNA by Wang and Davidson [Cold Spring Harbor Symp. Quant. Biol. 33, 409-415 (1968)] is treated as an oligomer-polymer interconversion. The dependence of equilibrium constant for this reaction on counterion concentration is in good agreement with that predicted by theory for an end-region totalling 24 nucleotides, the known length of the λ ends.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1978.360170112
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  • 2
    Electronic Resource
    Electronic Resource
    Association kinetics of site-specific protein-DNA interactions: Roles of nonspecific DNA sites and of the molecular location of the specific site (1989)
    New York : Wiley-Blackwell
    Biopolymers 28 (1989), S. 929-953 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We have applied the formalism developed previously for the kinetics of domain-localized reaction [S. Mazur and M. T. Record, Jr. (1986) Biopolymers 25, 985-1008] to describe complex mechanisms of association of a protein with a specific site on a large DNA molecule also containing many nonspecific binding sites. These nonspecific sites participate in the mechanism of formation of the specific complex through competitive binding and the facilitating mechanisms of sliding and transfer. The effects of localizing the sites in a domain are represented by a simple algebraic expression, and the sequence of interactions within the domain are described by equations closely related to a conventional, homogeneous solution mechanism. We apply this formalism to examine the interplay between sliding and direct transfer in domain-localized interactions in general and in the lac repressor-lac operator interaction in particular. Experimental investigation of the effect of the molecular location of the specific site (e.g., end vs middle of the polymer chain) on the kinetics of association may allow the contributions of sliding and direct transfer to be resolved.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360280503
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  • 3
    Electronic Resource
    Electronic Resource
    Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysisDedicated to Emeritus Professor Bruno H. Zimm, in whose laboratory one of us (MTR) began his study of the thermodynamic behavior of nucleic acid polyelectrolytes. (1991)
    New York : Wiley-Blackwell
    Biopolymers 31 (1991), S. 1593-1604 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Effects of salt concentration on the stabilities of oligonucleotide helices are analyzed directly in terms of ΔΓN→yN ≡ ΓyNden - ΓNnat, the difference in the salt-nucleotide phosphate preferential interaction coefficients for the denatured state, having yN phosphate charges, and for the native state, having N phosphate charges (y = 1 for hairpin denaturation and y = 0.5 for dimer denaturation). Previous experimental studies of the denaturation of hairpin oligo-nucleotides (having 18 〈 N 〈 44) indicate significant differences between ΔΓN→N and ΔΓ∞, the value determined for the denaturation of the corresponding polynucleotide. These differences are thermodynamic manifestations of the oligoelectrolyte end effect. In contrast, the available data on the denaturation of oligonucleotide dimer helices (N ≤ 22) imply that differences between ΔΓ∞ and ΔΓN→0.5N, and hence oligoelectrolyte end effects, are small or negligible. To determine the origin of these apparently conflicting implications concerning the importance of oligoelectrolyte end effects, we have calculated the N dependence of ΓN from grand canonical Monte Carlo simulations for an idealized model of the structure and charge distribution of each oligomer conformation. Our calculations are in quantitative agreement with the experimental finding for d(TA) hairpin oligomers that - ΔΓN→N decreases linearly as N-1 increases, and with the extant experimental determinations of ΔΓN→0.5N. These results provide an illustration of how the large electrostatic end effects exhibited by the hairpin denaturation data are masked when ΔΓ∞ is compared with values of ΔΓN→0.5N for short dimer helices (N ≤ 22). For 0.5N 〉 24, - ΔΓN→0.5N is predicted to be a linear function of N-1 whose slope has the opposite sign from, and is more salt-concentration dependent than, the corresponding slope of - ΔΓN→N as a function of N-1. Our calculations also yield predictions about the N dependences of the individual values of ΓN that can be tested by determining Donnan coefficients from membrane dialysis equilibrium experiments. For long enough hairpin and dimer oligonucleotides (yN ≥ 24), in either native or denatured forms, we predict that the (positive) difference Γ∞ - ΓN increases linearly with increasing N-1. For smaller values of N the difference Γ∞ - ΓN continues to increase with increasing N-1.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360311314
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  • 4
    Electronic Resource
    Electronic Resource
    Na+ effects on transitions of DNA and polynucleotides of variable linear charge density (1976)
    New York : Wiley-Blackwell
    Biopolymers 15 (1976), S. 893-915 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A range of linear charge densities of the ordered and disordered forms of DNA or polynucleotides can be obtained experimentally by acid or alkaline titration, or by the investigation of unusual complexes involving protonated bases or three-stranded helices. The variation of melting temperatures with Na+ concentration for various of these systems is known and in some cases is complemented by structural and thermodynamic information. We have extended the condensation-screening theory of Manning [Biopolymers, 11, 937-955 (1972)] to these systems. The stabilizing and destabilizing effects of Na+ (condensation and screening, respectively) and be independently varied, and the theory is successful in predicting the qualitative (in some cases, quanittative) behaviour that is observed. Comparison of theory and experiment indicates that the axial phosphate distance b for single-stranded polynucleotides increases with increasing pH. Values of the critical parameter ξ are obtained for the various polynucleotide structures. These values are essential for an understanding of ionic effects on charged ligand-polynucleotide interactions.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1976.360150507
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  • 5
    Electronic Resource
    Electronic Resource
    Kinetics of nonspecific binding reactions of proteins with DNA flexible coils: Site-based and molecule-based association reactions (1986)
    New York : Wiley-Blackwell
    Biopolymers 25 (1986), S. 985-1008 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Domain effects on the pseudo-first-order kinetics of the reversible and irreversible association of proteins or other ligands with nucleic acids containing multiple binding sites are treated using the classical reaction-diffusion equation applied to a spherical cell model of the nucleic acid solution and a diffuse-sphere model for the nucleic acid chain molecule. Both uniform and Gaussian distributions of chain segments are analyzed. In general, the details of the segment distribution do not have a major effect on the kinetics of association. Domain effects are best examined experimentally by determining the effect of the molecular weight of the nucleic acid on the kinetics of the association reaction. A theoretical framework is presented that permits such data to be analyzed simply. Kinetic studies over a wide range of nucleic acid molecular weights are required in order to separate the contributions of diffusion and reaction to the observed kinetics, and to determine the contributions of site-based and molecule-based elements to the rate constants.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360250603
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  • 6
    Electronic Resource
    Electronic Resource
    Mechanism for the aqueous acid decomposition of the formaldehyde derivative of cellulose xanthate (1965)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Applied Polymer Science 9 (1965), S. 1067-1072 
    Details
    ISSN: 0021-8995
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Kinetic equations for the decomposition of S-hydroxymethyl cellulose xanthate in the presence of acid and formaldehyde are derived. The assumed mechanism involves an equilibrium between the S-hydroxymethyl cellulose xanthate and cellulose xanthic acid and xanthate ion. Decomposition appears to proceed via interaction between the cellulose xanthate ion and hydrogen ion which form an activated complex that subsequently decomposes to cellulose and carbon disulfide. The equations derived show the proper dependence on acid and formaldehyde concentrations. An estimate of the equilibrium constant between cellulose xanthate and S-hydroxymethyl cellulose xanthate is calculated from the rate constants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/app.1965.070090322
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  • 7
    Electronic Resource
    Electronic Resource
    Electrostatic effects on polynucleotide transitions. I. Behavior at neutral pH (1967)
    New York : Wiley-Blackwell
    Biopolymers 5 (1967), S. 975-992 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: An approximate analytical expression for the electrostatic free energy of a polynucleo-tide in any of its possible ordered or random conformations is derived by integration of the screened-Coulomb potential energy function over all charge pairs in the structure. The electrostatic free energy of any form is found to be a linear function of the logarithm of the monovalent counterion concentration, in the range of low salt concentrations. Hence the electrostatic free energy difference between ordered and disordered forms in a polynucleotide structural transition is a linear function of the logarithm of the monovalent counterion concentration. A free energy balance applied to a two-state model for the transition then yields a linear dependence of the transition temperature Tm upon the logarithm of the counterion concentration. Calculation of the quantity dTm/d log M, where M is the monovalent counterion concentration, shows it to be a characteristic constant for a given transition, with a magnitude and sign proportional to the charge density difference between the ordered and disordered forms. Use of any one of several alternate, simple assumptions yields predicted dTm/d log M values in good agreement with experimental data for various polynucleotide transitions.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1967.360051010
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  • 8
    Electronic Resource
    Electronic Resource
    Electrostatic effects on polynucleotide transitions. II. Behavior of titrated systems (1967)
    New York : Wiley-Blackwell
    Biopolymers 5 (1967), S. 993-1008 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The theory developed in the previous paper to discuss changes in electrostatic free energies in polynucleotide order-disorder transitions is extended to cases where one or more of the participating species is titrated to some degree α. It is shown that, for any class of transition, the melting temperature Tm at constant pH is a linear function of the logarithm of the monovalent counterion concentration M, that at high salt the logarithm of the depression of the melting temperature by pH titration is proportional to the pH change, and that the stability of the ordered form as measured by its melting temperature at neutral pH, is a monotonic function of the quantity pHm - pK, where pHm and pK are the pH of melting and the monomer base pK, both measured under similar conditions of temperature and ionic strength. For the transition from double helix to coil, the dependences of Tm and dTm/d log M on pH are determined experimentally and compared with the qualitative predictions of the theory. It is found that dTm/dlog M, a measure of - ΔF̄el (the negative of the electrostatic free energy change in the transition), decreases with increasing pH. In acid solution, where the coil is more extensively prolonated than the helix, the change in electrostatic free energy in the transition is larger than at neutral pH. Conversely, in alkali the electrostatic five energy change is smaller than at neutral pH. Hence (dTm/d log M)acid 〉 (dTm/d log M neutral) 〉 (dTm/d log M)alkali. At Suffeciently high pH, dTm/d log M is observed to become negative, indicating that the electrostatic free energy change is positive in the transition of this region. Date from the literature on the ionic strength dependence of the melting temperature for the acid helices of poly rA, poly rC, and poly dC are also considered from the standpoint of the theory.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1967.360051011
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  • 9
    Electronic Resource
    Electronic Resource
    Kinetics of the helix-coil transition in DNA (1972)
    New York : Wiley-Blackwell
    Biopolymers 11 (1972), S. 1435-1484 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The kinetics of the helix-coil transition have been investigated for T2 and T7 phage DNA in a formamide-water-salt mixed solvent using a slow temperature perturbation technique (applicable to kinetic processes with rate constants ≤ 3 min-1). In this solvent degradation of the DNA is effectively suppressed. Complex kinetic curves are observed by absorbance and viscosity measurements for the response to denaturing perturbations in the transition region. Analysis of the decay curves indicates that the denaturation reaction in this time range can be treated as a first-order reaction with a variable first-order rate parameter, k, the derivative of the logarithm of the absorbance or viscosity change with respect to time. In the approach to denaturation equilibrium in the transition region, the rate parameter is determined only by the instantaneous extent of denaturation of the molecules. Near equilibrium, the rate parameter assumes a constant value characteristic of the equilibrium state. In this region, where the denaturation reaction proceeds as a simple first-order process, both the decay of absorbance (reflected local conformational change) and the decay of solution viscosity (reflecting macromolecular conformational change) are characterized by the same constant value of k. In 83% formamide, 0.3M Na+, the rate parameter k for T2 DNA decreases from an extrapolated value of 2.0 min-1 at 0% denaturation to 0.11 min-1 at 90% denaturation. Rate parameters determined for T7 DNA at the same counterion concentration and fraction of denaturation are approximately five times as large as those cited for T2 DNA, indicating an inverse proportionality of rate constant to molecular length. On the other hand, simple first-order kinetic responses with constant k are obtained for renaturing perturbations within the transition, indicating that the mechanism of rewinding differs, in most cases, from that of unwinding. Only in the limit of very small perturbations about a given equilibrium position are the rate constants k obtained from denaturing and renaturing perturbations equal. For perturbations of finite size, it appears possible that an intramolecular initiation or nucleation event may precede rewinding and limit the rate of this reaction. The rate parameters again are approximately inversely proportional to molecular weight. The one exception to the first-power dependence on molecular weight appears when temperature jumps are made upward into the post-transition region. Here the molecular-weight dependence is second power, but complications arising from the different strand-separation properties of T2 and T7 DNA's make interpretation difficult. The previously used model of friction-limited unwinding appears to fit all the observations except for the molecular-weight dependence.
    Additional Material: 24 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1972.360110711
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  • 10
    Electronic Resource
    Electronic Resource
    The strand-separation transition of T2 bacteriophage DNA (1974)
    New York : Wiley-Blackwell
    Biopolymers 13 (1974), S. 797-824 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Strand separation of T2 DNA has been investigated in a helix-destabilizing solvent. Temperature-shift experiments in which the conformation of the DNA is monitored by its viscosity, sedimentation behavior, and kinetics of helix formation show that a well-defined strand-separation transition follows the helix-coil transition usually observed by changes in absorbance. For T2 DNA, this strand-separation transition is 70% as broad as the helix-coil transition, and is characterized by extremely slow kinetics of conformational change in the population. Strand separation requires the expansion of the two-stranded coil observed at the end of the helix-coil transition. This expansion is apparently coupled with the disurption of the last remaining base pairs in the molecule. The expansion process increases the viscosity, and can be readily followed as a function of time and/or temperature. Subsequent separation of the expanded form into complementary strands results in a viscosity decrease, the net result of a reduction in hydrodynamic volume and the halving of the molecular weight. Only under conditions where the driving force for strand separation is large are these events at all synchronous in the population. When the kinetics of conformational change are complete in the strand-separation transition, a mixture of expanded forms and separate strands is observed; the breadth of the transition reflects differences in stability with respect to strand separation among the molecules in the population. The transition exhibits hysteresis and is not a reversible equilibrium between double-stranded and single-stranded forms. It appears that renucleation is kinetically forbidden within the strand-separation region.
    Additional Material: 18 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.1974.360130415
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