171
the subject of applications of Cd in dNA research has been treated in detail in a
number of excellent review works [9, 79–82], and our current paper is only a brief
attempt to highlight certain similarities and differences in regard to protein Cd. Just
like in the case of proteins, locally and globally distinct conformations may be accessible to a dNA chain—depending on its length, nucleotide sequence, and physicochemical conditions. dNA melting is a phenomenon of temperature-induced unfolding of the double-helix structure and an obvious equivalent of thermal denaturation of a protein. Because the melting causes disarray of the helical staircase holding nucleotide chromophores it is reflected by a simultaneous decrease of the Cotton
effect. however, temperature-induced denaturation is only an iceberg tip of plethora
of fascinating applications of Cd in nucleic acid research, most of which are related
to polymorphism of dNA helices. the right-handed B-type double helix is the most
common form of dNA and one out of several structures that can be induced in vitro
by varying co-solvent concentration and ionic strength in dNA solutions. transitions between these different helical structures may be conveniently probed by Cd
(Fig. 6.5). the naturally-occurring B-form converts into likewise right-handed but
of larger diameter A-form in the presence of certain organic solvents, such as trifluoroethanol (tFE). In Cd spectra of Cg- rich dNA this is typically reflected by a
shift of main positive band from ca 275 nm to 260 nm and simultaneous emergence
of a negative band below 220 nm. unlike A- and B-type double helices, the Z-form
of dNA is a left-handed helix. It may be formed from the B-type in presence of high
salt concentrations or cosolvents (depending on sequence). the reversal of helical
sense must cause pronounced changes in the Cd spectra, but their character again
depends on the exact covalent nature of the dNA chain (e.g. Ref. 82 vs. 83). In fact,
the A, B, and Z forms of double helix are the simplest aspects of dNA polymorphism. Circular dichroism has been successfully utilized to probe other nonclassical structures of dNA such as triplex, quadruplex, or parallel dNA. Expert review
works (for example that by maurizot [80]) treat these problems in detail.
Perturbations in dNA conformation may follow from more physiological factors
than drastic changes in solvation that are often used in vitro—for example through
docking interactions with proteins or small ligands specifically binding to nucleic
acids. there are excellent reviews devoted to application of Cd to protein-dNA
interactions available [13, 81] and therefore this complex subject will not be discussed in this brief review.
6.5 CD and Absolute Configuration of Biologically
Active Molecules
For many years, Cd has been used to establish unknown absolute configurations
of synthetic or naturally occuring chiral compounds (in many cases with some
biological significance, for example pharmaceutical potential). At first, such assignment relied on empirical rules such as quadrant or octant rule, which naturally
limited the range of application of Cd in this field. With advancement of theoretical
6 Electronic Circular dichroism Spectroscopy in Structural Analysis …
the subject of applications of Cd in dNA research has been treated in detail in a
number of excellent review works [9, 79–82], and our current paper is only a brief
attempt to highlight certain similarities and differences in regard to protein Cd. Just
like in the case of proteins, locally and globally distinct conformations may be accessible to a dNA chain—depending on its length, nucleotide sequence, and physicochemical conditions. dNA melting is a phenomenon of temperature-induced unfolding of the double-helix structure and an obvious equivalent of thermal denaturation of a protein. Because the melting causes disarray of the helical staircase holding nucleotide chromophores it is reflected by a simultaneous decrease of the Cotton
effect. however, temperature-induced denaturation is only an iceberg tip of plethora
of fascinating applications of Cd in nucleic acid research, most of which are related
to polymorphism of dNA helices. the right-handed B-type double helix is the most
common form of dNA and one out of several structures that can be induced in vitro
by varying co-solvent concentration and ionic strength in dNA solutions. transitions between these different helical structures may be conveniently probed by Cd
(Fig. 6.5). the naturally-occurring B-form converts into likewise right-handed but
of larger diameter A-form in the presence of certain organic solvents, such as trifluoroethanol (tFE). In Cd spectra of Cg- rich dNA this is typically reflected by a
shift of main positive band from ca 275 nm to 260 nm and simultaneous emergence
of a negative band below 220 nm. unlike A- and B-type double helices, the Z-form
of dNA is a left-handed helix. It may be formed from the B-type in presence of high
salt concentrations or cosolvents (depending on sequence). the reversal of helical
sense must cause pronounced changes in the Cd spectra, but their character again
depends on the exact covalent nature of the dNA chain (e.g. Ref. 82 vs. 83). In fact,
the A, B, and Z forms of double helix are the simplest aspects of dNA polymorphism. Circular dichroism has been successfully utilized to probe other nonclassical structures of dNA such as triplex, quadruplex, or parallel dNA. Expert review
works (for example that by maurizot [80]) treat these problems in detail.
Perturbations in dNA conformation may follow from more physiological factors
than drastic changes in solvation that are often used in vitro—for example through
docking interactions with proteins or small ligands specifically binding to nucleic
acids. there are excellent reviews devoted to application of Cd to protein-dNA
interactions available [13, 81] and therefore this complex subject will not be discussed in this brief review.
6.5 CD and Absolute Configuration of Biologically
Active Molecules
For many years, Cd has been used to establish unknown absolute configurations
of synthetic or naturally occuring chiral compounds (in many cases with some
biological significance, for example pharmaceutical potential). At first, such assignment relied on empirical rules such as quadrant or octant rule, which naturally
limited the range of application of Cd in this field. With advancement of theoretical
6 Electronic Circular dichroism Spectroscopy in Structural Analysis …