24
M. P. Evstigneev and A. V. Shestopalova
ture, and structural variations of the DNA—ligand complexes in aqueous solution
[23–28].
IR and Raman spectroscopies are able to provide information on the formation of
hydrogen bonds in solution. It has long been known that the formation of hydrogen
bonds between the proton donor (OH, NH, NH 2 , CH) and acceptor (C = O, C–O,
C–N, C = N) groups is accompanied by a low-frequency shift, rising in intensity
and increase in the half-width of the absorption bands of stretching vibrations in
the IR spectrum [29, 30]. At the same time the absorption bands of deformation
vibrations (e.g. NH 2 - and OH-groups) experience high-frequency shifts [31]. These
spectral features are considered as a direct evidence of H-bonds formation between
the interacting molecules in solution [32]. Thus, the groups of atoms involved in
stabilization of different types of DNA—ligand complexes can be identified by the
vibrational spectroscopy [33–35]. In particular, analysis of Raman spectra allows
to identify the atomic groups of the drugs forming hydrogen bonds with donor or
acceptor atomic groups of DNA in all possible types of DNA-drug complexes [36,
37], and to determine, for example, the unwinding of double-stranded B-DNA induced by drug intercalation [38] or structural transition of DNA from B- to A-like
conformation accompanying the DNA-ligand complexation [39].
2.2.3 Hydration
Since the formation of DNA—ligand complex occurs in water environment and
brings one of the most significant contributions to stabilization of the DNA-ligand
complexes, it is important to carry out analysis of the role, which water plays in the
ligand binding processes [40–42]. From a practical point of view, understanding of
hydration is valuable for rational design of novel DNA—binding drugs with predictable affinity and specificity to selected sequences of nucleic acid structures [43].
Investigations of the interaction between water molecules and DNA—ligand
complexes in diluted solutions face serious difficulties due to the fact that the bound
water is present only in insignificant amounts in solution. This fact implies the need
to utilize highly sensitive physical methods for the study of water involvement in
the complexation process. This is the reason why there is still a lack of reliable information on the distribution of water molecules in the hydration shells of various
complexes, although the investigations of water surrounding of nucleic acid—ligand complexes have so far been carried out using numerous methods including
X-ray crystallography [44], osmotic stress [43, 45], volumetry [46, 47] and molecular modeling methods [48–50]. In the IR spectroscopy the main difficulties are
associated with the strong OH vibration of water molecules. This problem may be
resolved by applying this method with respect to DNA—water systems prepared in
wet films with changing water content [51–54]. Analyzing the changes in IR spectra
which occur in several frequency modes (e.g. the stretching vibrations of OH- or
OD-groups, the absorption band of bases—double and multiple bands, the absorption band of sugar-phosphate backbone) with an increase of the relative humidity,
M. P. Evstigneev and A. V. Shestopalova
ture, and structural variations of the DNA—ligand complexes in aqueous solution
[23–28].
IR and Raman spectroscopies are able to provide information on the formation of
hydrogen bonds in solution. It has long been known that the formation of hydrogen
bonds between the proton donor (OH, NH, NH 2 , CH) and acceptor (C = O, C–O,
C–N, C = N) groups is accompanied by a low-frequency shift, rising in intensity
and increase in the half-width of the absorption bands of stretching vibrations in
the IR spectrum [29, 30]. At the same time the absorption bands of deformation
vibrations (e.g. NH 2 - and OH-groups) experience high-frequency shifts [31]. These
spectral features are considered as a direct evidence of H-bonds formation between
the interacting molecules in solution [32]. Thus, the groups of atoms involved in
stabilization of different types of DNA—ligand complexes can be identified by the
vibrational spectroscopy [33–35]. In particular, analysis of Raman spectra allows
to identify the atomic groups of the drugs forming hydrogen bonds with donor or
acceptor atomic groups of DNA in all possible types of DNA-drug complexes [36,
37], and to determine, for example, the unwinding of double-stranded B-DNA induced by drug intercalation [38] or structural transition of DNA from B- to A-like
conformation accompanying the DNA-ligand complexation [39].
2.2.3 Hydration
Since the formation of DNA—ligand complex occurs in water environment and
brings one of the most significant contributions to stabilization of the DNA-ligand
complexes, it is important to carry out analysis of the role, which water plays in the
ligand binding processes [40–42]. From a practical point of view, understanding of
hydration is valuable for rational design of novel DNA—binding drugs with predictable affinity and specificity to selected sequences of nucleic acid structures [43].
Investigations of the interaction between water molecules and DNA—ligand
complexes in diluted solutions face serious difficulties due to the fact that the bound
water is present only in insignificant amounts in solution. This fact implies the need
to utilize highly sensitive physical methods for the study of water involvement in
the complexation process. This is the reason why there is still a lack of reliable information on the distribution of water molecules in the hydration shells of various
complexes, although the investigations of water surrounding of nucleic acid—ligand complexes have so far been carried out using numerous methods including
X-ray crystallography [44], osmotic stress [43, 45], volumetry [46, 47] and molecular modeling methods [48–50]. In the IR spectroscopy the main difficulties are
associated with the strong OH vibration of water molecules. This problem may be
resolved by applying this method with respect to DNA—water systems prepared in
wet films with changing water content [51–54]. Analyzing the changes in IR spectra
which occur in several frequency modes (e.g. the stretching vibrations of OH- or
OD-groups, the absorption band of bases—double and multiple bands, the absorption band of sugar-phosphate backbone) with an increase of the relative humidity,