Analysis of DNA-ligand binding in solution and on biochips

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,...

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Bibliographic Details
Published in:Biophysics (Oxford) 2011-12, Vol.56 (6), p.1033-1040
Main Authors: Khodykov, M. V., Anashkina, A. A., Golovkin, M. V., Matveeva, O. V., Nechipurenko, Yu. D.
Format: Article
Language:English
Subjects:
Adsorption
Biological and Medical Physics
Biophysics
Deoxyribonucleic acid
DNA
Hybridization
Mathematical models
Molecular Biophysics
Physics
Physics and Astronomy
Thermodynamics
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Summary: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.
ISSN:0006-3509
1555-6654
DOI:10.1134/S000635091106008X