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  • 1
    Electronic Resource
    Electronic Resource
    Theory of the mobility-shift assay of nonspecific protein-DNA complexes governed by conditional probabilities: The HU:DNA complex (1995)
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 881-887 
    Details
    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
    URL: http://dx.doi.org/10.1002/elps.11501601148
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Theory and practice of isoelectric focusing of interacting systems (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 1577-1585 
    Details
    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
    URL: http://dx.doi.org/10.1002/elps.1150191010
    Library Location Call Number Volume/Issue/Year Availability
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    Paper (German National Licenses)
    Fulltext
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