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The porphyrin handbook - Kadish K.M.

Kadish K.M. The porphyrin handbook - Academic press, 2000. - 368 p.
Download (direct link): kadishsmishgulilard2000.djvu
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studied system is the binding of the cationic porphyrin, 5,10,15,20-
tetrakis[W-
46 / Porphyrins and Metalloporphyrins as Receptor Models
inethylpyridinium-4-ly]porphyrin 52 and its metal complexes, to DNAs. The
interactions and binding modes were studied by UV-Vis, CD, NMR, and
resonance light-scattering spectroscopies. Fiel proposed a three-site
binding model, where porphyrin can interact with DNA via (I)
intercalation to the base pairs; (2) outside binding with self-stacking
of porphyrins; and (3) random outside binding.41 The preference for these
binding modes is dependent upon the central metal of the porphyrin,
substituents on the poq^hyrin, DNA structures and ionic strength of the
media. For intercalation to occur, "thin" porphyrins, such as free-base
porphyrins and Cu(II), Pt(II) or Ni(II) porphyrins, that have no axial
ligand are required. On the other hand. Zn(II), Fe(III). Mn(II) and
Co(II) porphyrins accept an axial ligand, and were not bound (o DNA by
intercalation.
Table 6 lists association constants between porphyrins and nucleic
acids. Equilibrium constants between H2(TMpyP-4) (52) and Cu(TMpyP-4)
(88) with a synthetic polymer poly(dG-dC) were estimated to be 7.7 x 105
M ~1 and 8.0 x lO-'M-1, respectively, based on McGhee-von Hippel
analysis.42 The equilibrium constants were ionic-strength dependent. It
was observed that at 2 M ionic strength, the free-base poq}hyrin 52
almost completely dissociates from DNA, poly(dA-dT) and poly(dG-dC).
Therefore electrostatic interactions are the important driving force.
Kinetic studies were carried out for the above system
-N*-
87
using stopped-flow and temperature-jump techniques. The binding of both
axially and nonaxially liganded porphyrins to AT sites was too rapid to
be measured, whereas with GC sites the interaction of the nonaxially
liganded porphyrin occurred within milliseconds. This observation is
consistent with the formation of an intercalated complex only at GC sites
with porphyrins bearing no axial ligands. Rate constants for association
and dissociation of the H2(TMpyP-4)(52)/poly(dG-dC) complex were 3.7 x HP
M -1 s ~ 1 and 1.8 s - 1, respectively.
It is interesting to note that tetrakis(/V-methylpyridinium-
2-yl)porphyrin 91 scarcely interacts with DNA.42 Because the rotation
about the single bond between pyridinium groups and porphyrin is severely
restricted for the 2-pyridiniumyl derivative compared wilh the 4-
pyridiniumyl derivative, it may be that the eoplanar structure of
porphyrins and the pyridinium group required for an intercalated complex.
For the porphyrin oulside binding, poly[(dA-dT)|3 and poly[(dG-dC)h
behaved differently.43 45 The binding of 53 to poly[(dA-dT)J? was about
200 times more favorable than to poly[(dG-dC)]2. UV-CD studies revealed
that the structure of poly[(dA-dT)]2 was distorted upon binding, while
that of poly[(dG-dC)h was not. These results indicate that the outside
binding of porphyrins preferentially occurs at the more flexible AT site
than at the GC site. This
88* M = Cu(ll)
89 M = Cu(ll)
91 M " H2
90' M = H2
92: M = Cu(ll)
J
305
3
94
-,
selectivity could be correlated with the rigid arrangement of positive
charges within the porphyrin framework. However, Marzilli et al.9b
reported competitive binding studies of "tentacle" porphyrin 93 which
revealed that the flexible porphyrin also showed preferential binding to
poly[(dA-dT)]2 over poly](dG-dC)]2. Similar AT preference was reported
for the manganese and iron complexes of 52.97 94
Williams et al.m) reported the 2.4 A X-ray structure of a complex
between a hexamer duplex, [d(CGATCG)J2, and Cu"(TMPyP-4). The porphyrin
molecules intercalate at the C-G steps of [d(CGATCG)J2 such that two
porphyrins bind to each hexamer duplex. The porphyrin binds between the
and G of 5' TCG 3' and extrude the of 5' CGA 3'. The copper porphyrin
is located within the helical stack, with the copper atom near the
helical axis. Two pyridyl rings are located in the minor groove, and
electrostatic interactions between the positive charges of the pyridyl
rings and the negative charges of the phosphate groups particularly
stabilize the complex, as seen from the short distances between the
pyridyl nitrogens and the phosphate oxygens.
H. SOLVENT EFFECTS ON MOLECULAR RECOGNITION
It is widely recognized that binding processes are dependent upon the
solvent used. For example, the enthalpy and entropy changes in complex
formation between ( - )-63 and L-valine methyl ester were -21.3 kJ/mol
and +10.5J/K/ mol at 293 K, respectively, in CHC13 containing 0.5%
ethanol as a stabilizer; they were -125.5 kJ/mol and
- 310.9J/K/mol in ethanol-free CH2C12, respectively, and were - 94.1
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