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2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions
2.2.1 UV-VIS Spectroscopy
Absorption UV-VIS spectroscopy is one of the most widespread experimental
methods used in molecular biology and biophysics for qualitative and quantitative
studies of the interaction of biologically active ligands with DNA. This experimental method enables to identify the formation of complexes, to evaluate their complexation constants, to determine different types of ligand states in solution (e.g.
free and bound with polymer matrix by various modes) on the basis of the shape
and positions of the maxima in the corresponding spectra, to calculate the size of the
binding site and the sequence specificity [10–17]. The changes in absorption spectra
on addition of drugs to DNA solutions may be used for identification of different
types of ligand complexation (e.g. intercalation or major/minor groove binding).
The method of spectrophotometric titration is usually used for detailed analysis
of the binding modes and the structures of the molecular complexes [18]. Concentration dependencies obtained during the titration of the DNA—ligand complexes
may be used for calculation of the binding parameters. The most important factor
in correct determination of these parameters is the choice of the model of complexation, in which all physically possible binding modes (intercalation, binding with
one of the DNA grooves, weak binding or electrostatic interactions of the ligand
cation with negatively charged phosphate groups of the polynucleotide) should be
taken into account. When a suitable model (or the most probable models) is selected, the equations, determining the relation between the equilibrium concentrations of the molecular components and the interaction parameters, may be used for
quantitative description of the titration curve [19–21].
Thermodynamic parameters and the process of thermal denaturation of the
drug—DNA complexes can be systematically studied by spectrophotometric
method. Such approach yields a thermodynamic profile, i.e. standard free energy,
enthalpy and entropy changes in ligand-DNA reaction of binding, using the van’t
Hoff plot based on determining the value of equilibrium binding constant at various temperatures. These thermodynamic parameters allow to further evaluate the
enthalpic and entropic contributions to the free energy change in the DNA complexation process [22].
However, the most fruitful outcome can be achieved by a combination of the
UV-VIS spectroscopy with other experimental methods.
2.2.2 Infrared and Raman Vibrational Spectroscopy
Among different physical methods of investigation of specific structural features
and intermolecular interactions of nucleic acids with drugs and water, the Infrared
(IR) and Raman vibrational spectroscopies occupy very important position. Both
of these methods can effectively probe structural details of solution complexes between the drugs and DNA molecules of genomic size, and are used to determine the
ligand binding mode, binding affinity, sequence selectivity, DNA secondary struc-
2 Structure, Thermodynamics and Energetics of Drug-DNA Interactions
2.2.1 UV-VIS Spectroscopy
Absorption UV-VIS spectroscopy is one of the most widespread experimental
methods used in molecular biology and biophysics for qualitative and quantitative
studies of the interaction of biologically active ligands with DNA. This experimental method enables to identify the formation of complexes, to evaluate their complexation constants, to determine different types of ligand states in solution (e.g.
free and bound with polymer matrix by various modes) on the basis of the shape
and positions of the maxima in the corresponding spectra, to calculate the size of the
binding site and the sequence specificity [10–17]. The changes in absorption spectra
on addition of drugs to DNA solutions may be used for identification of different
types of ligand complexation (e.g. intercalation or major/minor groove binding).
The method of spectrophotometric titration is usually used for detailed analysis
of the binding modes and the structures of the molecular complexes [18]. Concentration dependencies obtained during the titration of the DNA—ligand complexes
may be used for calculation of the binding parameters. The most important factor
in correct determination of these parameters is the choice of the model of complexation, in which all physically possible binding modes (intercalation, binding with
one of the DNA grooves, weak binding or electrostatic interactions of the ligand
cation with negatively charged phosphate groups of the polynucleotide) should be
taken into account. When a suitable model (or the most probable models) is selected, the equations, determining the relation between the equilibrium concentrations of the molecular components and the interaction parameters, may be used for
quantitative description of the titration curve [19–21].
Thermodynamic parameters and the process of thermal denaturation of the
drug—DNA complexes can be systematically studied by spectrophotometric
method. Such approach yields a thermodynamic profile, i.e. standard free energy,
enthalpy and entropy changes in ligand-DNA reaction of binding, using the van’t
Hoff plot based on determining the value of equilibrium binding constant at various temperatures. These thermodynamic parameters allow to further evaluate the
enthalpic and entropic contributions to the free energy change in the DNA complexation process [22].
However, the most fruitful outcome can be achieved by a combination of the
UV-VIS spectroscopy with other experimental methods.
2.2.2 Infrared and Raman Vibrational Spectroscopy
Among different physical methods of investigation of specific structural features
and intermolecular interactions of nucleic acids with drugs and water, the Infrared
(IR) and Raman vibrational spectroscopies occupy very important position. Both
of these methods can effectively probe structural details of solution complexes between the drugs and DNA molecules of genomic size, and are used to determine the
ligand binding mode, binding affinity, sequence selectivity, DNA secondary struc-