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Analysis of DNA-ligand binding in solution and on biochips

  • Molecular Biophysics
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Abstract

Ligand binding to DNA, as well as to microarrays, requires a system approach to description and analysis. This type of approach implies a fixed sequence of operations. Firstly, it is necessary to make a description of a binding scheme that realizes ligand and polymer in common spatial way. Secondly, a physical model of binding is required. Thirdly, a mathematical binding model should be constructed on the basis of the binding scheme and the physical model of binding. Every analysis of experimental data needs this preliminary work. A mathematical apparatus and classification of binding models have to follow on. Classification of different binding isotherms by different binding models is the direct problem. The inverse problem is a reconstruction of parameters of a binding model by experimental binding isotherm curves. The inverse problem can only be solved after solving the direct problem. An example of classification of binding models by oligonucleotides or proteins binding cooperativity and polymer properties like homo-or heteropolymer is presented.

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Authors and Affiliations

  1. Moscow Institute of Physics and Technology, Moscow Region, 141700, Russia

    M. V. Khodykov

  2. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia

    A. A. Anashkina, O. V. Matveeva & Yu. D. Nechipurenko

  3. Skobeltsyn Institute of Nuclear Physics of Moscow State University, Moscow, 119991, Russia

    M. V. Golovkin

  4. Faculty of Physics, Moscow State University, Moscow, 119992, Russia

    Yu. D. Nechipurenko

Authors
  1. M. V. Khodykov
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  2. A. A. Anashkina
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  3. M. V. Golovkin
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  4. O. V. Matveeva
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  5. Yu. D. Nechipurenko
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Correspondence to M. V. Khodykov.

Additional information

Original Russian Text © M.V. Khodykov, A.A. Anashkina, M.V. Golovkin, O.V. Matveeva, Yu.D. Nechipurenko, 2011, published in Biofizika, 2011, Vol. 56, No. 6, pp. 1053–1061.

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Khodykov, M.V., Anashkina, A.A., Golovkin, M.V. et al. Analysis of DNA-ligand binding in solution and on biochips. BIOPHYSICS 56, 1033–1040 (2011). https://doi.org/10.1134/S000635091106008X

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  • DOI: https://doi.org/10.1134/S000635091106008X

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