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  • 1
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 71 (1949), S. 2687-2691 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 0173-0835
    Keywords: Mobility-shift assay ; Retardation analysis ; Nonspecific protein-DNA complexes ; Conditional probabilities ; Gel cage ; Histone-like bacterial protein (HU) ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Complexes of an 88 bp DNA and the HU protein were studied by both experimental and theoretical electrophoretic mobility-shift analyses. Experimental analysis defined the stoichiometry of binding and estimated an apparent intrinsic dissociation constant (Kd = 1 to 3 × 10-7 M) for the HU:DNA complexes. The theory of conditional probabilities was applied to the binding of HU to DNA in order to fix the initial equilibrium composition of mixtures to be assayed theoretically by the mobility-shift procedure. Electrophoretic mobility-shift patterns were obtained by numerical solution of a set of simultaneous transport-reaction equations, in which the chemical kinetic term is formulated in terms of dissociation of the different DNA:HU complexes in gel cages. The computed patterns simulated the experimental patterns describing the titration of a fixed concentration of an 88 bp DNA fragment with dimeric HU. These insightful results provide guidelines for interpretation of the electrophoretic behavior of systems in which a ligand binds nonspecifically to DNA. In particular, the narrow unresolved zone observed both experimentally and theoretically beyond 50-60% saturation is a reaction zone characteristic of noncooperative ligand-binding governed by conditional probabilities. The discrepancy between the theoretically assigned and experimental values of the intrinsic binding constant is attributed to an HU-induced change in the conformation of DNA.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0173-0835
    Keywords: Mobility-shift assay ; Retardation analysis ; Nonspecific protein-DNA complexes ; Histone-like bacterial protein ; Cooperative binding ; Gel cage ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The simulated electrophoretic mobility-shift behavior of a model system, in which the nonspecific binding of a protein to a DNA fragment is cooperative, was compared with the experimental behavior of the DNA: histone-like bacterial protein (HU) system. It was concluded that the binding of HU to an 88 bp DNA fragment is, at least, not highly cooperative. The theory of mobility-shift analysis was extended even further to encompass high affinity sequence-specific binding of protein to a DNA fragment followed by weak nonspecific binding, the latter governed by conditional probabilities. In addition to featuring a ladder of incremental protein-DNA complexes, the computed mobility-shift patterns placed emphasis upon stabilization of weak, nonspecific complexes in gel cages.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 1336-1340 
    ISSN: 0173-0835
    Keywords: Computer simulations ; DNA ; Dispersion ; Asymmetry ; Mobility-shift assay ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Incorporation of the dispersion coefficient into the theory of the mobility-shift assay for DNA-protein complexes was highly successful largely due to increased mathematical rigor. A model simulating electrophoretic migration of DNA across the phase boundary between the initial zone of macromolecule and the gel lane predicts the peak asymmetry observed experimentally. It also predicts that, under the agency of the dispersion coefficient, the peak will become progressively more symmetrical during migration along the gel lane.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 1577-1585 
    ISSN: 0173-0835
    Keywords: Isoelectric focusing ; Interacting systems ; Theory and practice ; Computer simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The theory of mass transport coupled to reversible protein interactions forms the basis for computer simulation of the isoelectric focusing behavior of several model systems. These include pH-dependent conformational transition, carrier ampholyte-induced interactions and protein-ligand interactions. The computational results compare favorably with experimental observations. In addition, a method is formulated for an isoelectric focusing procedure which enables determination of intrinsic ligand-binding constants for statistical binding of a charged ligand, binding to heterogeneous sites, and cooperative binding.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 14 (1993), S. 669-679 
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The theory of mass transport coupled to reversible interactions under chemical kinetic control forms the basis for computer simulation of the electrophoretic mobility-shift behavior of binary protein-DNA complexes. Several systems have been modeled in terms of either (i) specific binding of a protein molecule to a single site on the DNA molecule; (ii) cooperative binding to two or three sites; (iii) noncooperative binding to two sites, both of which bind protein with equal affinity; (iv) statistical binding to multiple sites having identical intrinsic binding constants; or (v) protein-induced DNA loop formation. Both models (iii) and (v) embody the concept of reversible isomerization of protein-DNA complexes. The resulting simulations have provided fundamental information concerning (i) the factors governing the electrophoretic persistence and separation of protein-DNA complexes; (ii) the shape of experimental mobility-shift patterns; (iii) the generation of the protein-DNA ladder upon titration, for example, of the 203-base pair operator with lac repressor; and (iv) the theoretical bases for quantitative interpretation of the patterns in terms of thermodynamic and kinetic parameters. The practical implications of these findings are discussed.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 127-141 
    ISSN: 0173-0835
    Keywords: Mobility-shift assay ; Retardation analysis ; Protein-DNA complexes ; Computer simulations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The theory of mass transport coupled to revesible macromolecular interactions under chemical kinetic control forms the basis for computer simulation of the electrophoretic mobility-shift behavior of protein-DNA complexes. Model systems include (i) specific binding of a univalent protein molecule to a single site on the DNA molecule; (ii) the putative cage effect; (iii) cooperative binding to multiple sites; (iv) formation of looped complexes of 1:1 and 2:1 stoichiometry; (v) noncooperative and cooperative, nonspecific binding modes; and (vi) binding of dimerizing transcriptional factors to response elements of target genes. Favorable comparison of simulated with experimental mobility-shift behavior indicates that the phenomenological mechanisms, whereby observed mobility-shift patterns are generated during electrophoresis, are embodies in the theory. These studies have provided guidelines for definitive interpretation of mobility-shift assays and for the design of experiments to develop a detailed understanding of the particular system under investigation.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 1535-1536 
    ISSN: 0173-0835
    Keywords: Mobility-shift assay ; Nonspecific protein-DNA complexes ; Gel cage ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Theoretical mobility-shift patterns are computed by solution of conservation equations for electrophoresis coupled with chemical reaction. The chemical reaction term is often formulated in terms of dissociation of the protein-DNA complex in a gel cage. This formulation assumes that once the dissociated protein escapes the cage, it goes down a sink and is totally lost. This implies that the concentration of the escaped protein is too low to affect sign ficantly the rates of protein-DNA association along its migration pathway.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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