Thermal analysis of ligand-DNA interaction: determination of binding parameters
The review discusses the methods of thermodynamic analysis of reactions of non-covalent binding of biologically active compounds with DNA, which is a key constituent of cell chromatin. Knowledge of thermodynamic profile of ligand binding with nucleic acids is important for understanding the mechanis...
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| Format: | Article |
| Language: | English |
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AIMS Press
2015-09-01
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| Series: | AIMS Biophysics |
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| Online Access: | http://www.aimspress.com/biophysics/article/410/fulltext.html |
| _version_ | 1811344204789448704 |
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| author | Ekaterina Bereznyak Natalia Gladkovskaya Evgeniy Dukhopelnykov Anastasiya Gerus Anastasiya Lantushenko Maxim Evstigneev |
| author_facet | Ekaterina Bereznyak Natalia Gladkovskaya Evgeniy Dukhopelnykov Anastasiya Gerus Anastasiya Lantushenko Maxim Evstigneev |
| author_sort | Ekaterina Bereznyak |
| collection | DOAJ |
| description | The review discusses the methods of thermodynamic analysis of reactions of non-covalent binding of biologically active compounds with DNA, which is a key constituent of cell chromatin. Knowledge of thermodynamic profile of ligand binding with nucleic acids is important for understanding the mechanism of medico-biological action of the currently existing drugs and for designing of new drugs with improved medical effect. Thermodynamic analysis of ligand binding with DNA is based on analysis of experimentally measured changes of Gibbs free energy (Δ<i>G</i>), enthalpy (Δ<i>H</i>), entropy (Δ<i>S</i>) and heat capacity (Δ<i>C<sub>р</sub></i>). Right selection of the methods of measurement of these parameters and understanding of limitations of currently existing approaches for numerical data analysis are crucially important for correct interpretation of the obtained results and getting insight into the mechanism of drug-DNA interaction. In the present work the currently existing methods of determination of thermodynamic parameters of ligand binding with DNA were divided into two main groups. The first group is associated with the approaches used in cases when the heating of the system does not cause melting of the biopolymer. The main focus is given to the second group of the methods which are based on description of helix-coil transition of DNA-ligand complexes with further comparison of the same transition for «free» biopolymer. The methods of computation of the binding parameters utilizing the Ising-type models and models based on the equations of chemical equilibrium are discussed. |
| first_indexed | 2024-04-13T19:43:38Z |
| format | Article |
| id | doaj.art-d1f8c7f5d6f946b6a510835f3fbaf204 |
| institution | Directory Open Access Journal |
| issn | 2377-9098 |
| language | English |
| last_indexed | 2024-04-13T19:43:38Z |
| publishDate | 2015-09-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Biophysics |
| spelling | doaj.art-d1f8c7f5d6f946b6a510835f3fbaf2042022-12-22T02:32:47ZengAIMS PressAIMS Biophysics2377-90982015-09-012442344010.3934/biophy.2015.4.423201504423Thermal analysis of ligand-DNA interaction: determination of binding parametersEkaterina Bereznyak0Natalia Gladkovskaya1Evgeniy Dukhopelnykov2Anastasiya Gerus3Anastasiya Lantushenko4Maxim EvstigneevInstitute for Radiophysics and Electronics NAS of Ukraine, 12 Ak. Proskura Str., Kharkov, 61085, UkraineInstitute for Radiophysics and Electronics NAS of Ukraine, 12 Ak. Proskura Str., Kharkov, 61085, UkraineInstitute for Radiophysics and Electronics NAS of Ukraine, 12 Ak. Proskura Str., Kharkov, 61085, UkraineInstitute for Radiophysics and Electronics NAS of Ukraine, 12 Ak. Proskura Str., Kharkov, 61085, UkraineDepartment of Physics, Sevastopol State University, Universitetskaya 33, Sevastopol 299053, RussiaThe review discusses the methods of thermodynamic analysis of reactions of non-covalent binding of biologically active compounds with DNA, which is a key constituent of cell chromatin. Knowledge of thermodynamic profile of ligand binding with nucleic acids is important for understanding the mechanism of medico-biological action of the currently existing drugs and for designing of new drugs with improved medical effect. Thermodynamic analysis of ligand binding with DNA is based on analysis of experimentally measured changes of Gibbs free energy (Δ<i>G</i>), enthalpy (Δ<i>H</i>), entropy (Δ<i>S</i>) and heat capacity (Δ<i>C<sub>р</sub></i>). Right selection of the methods of measurement of these parameters and understanding of limitations of currently existing approaches for numerical data analysis are crucially important for correct interpretation of the obtained results and getting insight into the mechanism of drug-DNA interaction. In the present work the currently existing methods of determination of thermodynamic parameters of ligand binding with DNA were divided into two main groups. The first group is associated with the approaches used in cases when the heating of the system does not cause melting of the biopolymer. The main focus is given to the second group of the methods which are based on description of helix-coil transition of DNA-ligand complexes with further comparison of the same transition for «free» biopolymer. The methods of computation of the binding parameters utilizing the Ising-type models and models based on the equations of chemical equilibrium are discussed.http://www.aimspress.com/biophysics/article/410/fulltext.htmlDNAligandmelting thermodynamicsbinding parameterscalorimetryUV-spectroscopy |
| spellingShingle | Ekaterina Bereznyak Natalia Gladkovskaya Evgeniy Dukhopelnykov Anastasiya Gerus Anastasiya Lantushenko Maxim Evstigneev Thermal analysis of ligand-DNA interaction: determination of binding parameters AIMS Biophysics DNA ligand melting thermodynamics binding parameters calorimetry UV-spectroscopy |
| title | Thermal analysis of ligand-DNA interaction: determination of binding parameters |
| title_full | Thermal analysis of ligand-DNA interaction: determination of binding parameters |
| title_fullStr | Thermal analysis of ligand-DNA interaction: determination of binding parameters |
| title_full_unstemmed | Thermal analysis of ligand-DNA interaction: determination of binding parameters |
| title_short | Thermal analysis of ligand-DNA interaction: determination of binding parameters |
| title_sort | thermal analysis of ligand dna interaction determination of binding parameters |
| topic | DNA ligand melting thermodynamics binding parameters calorimetry UV-spectroscopy |
| url | http://www.aimspress.com/biophysics/article/410/fulltext.html |
| work_keys_str_mv | AT ekaterinabereznyak thermalanalysisofliganddnainteractiondeterminationofbindingparameters AT nataliagladkovskaya thermalanalysisofliganddnainteractiondeterminationofbindingparameters AT evgeniydukhopelnykov thermalanalysisofliganddnainteractiondeterminationofbindingparameters AT anastasiyagerus thermalanalysisofliganddnainteractiondeterminationofbindingparameters AT anastasiyalantushenko thermalanalysisofliganddnainteractiondeterminationofbindingparameters AT maximevstigneev thermalanalysisofliganddnainteractiondeterminationofbindingparameters |