Chemistry Reference
In-Depth Information
The third binding mode is suggested by absorbance value attained by the
porphyrin-DNA complexes upon cooling to room temperature after the melting
experiments. In all cases analyzed (different molar ratio of porphyrin/DNA and
ionic strength), the Soret absorption values tend to be lower than the initial values
obtained upon mixing the two components, DNA and porphyrin. This indicates an
increase in binding of H
2
TMPyP4 to denatured DNA (Fig.
3
).
The presence of the sterically bulky
N-
methylpyridyl groups might be expected
to hinder the classical modes of intercalation as shown by molecules such as
proflavine or ethidium; however, another evidence of this binding mode has been
demonstrated by Fiel and Munson [
17
]. They showed by electrophoresis experiment
that closed circular supercoiled DNA from ColE1 in the presence of H
2
TMPyP4
migrates to relaxed circular DNA form. This latter experiment demonstrated the
ability of H
2
TMPyP4 to unwind closed circular supercoiled DNA, a feature diag-
nostic for intercalation of this compound into DNA [
18
-
20
]. They carried out the
same experiment in the presence of FeTMPyP4 which is not expected to intercalate
for steric reason due to the fact that tetrapyrrole rings are puckered to accommodate
the Fe(III) bound to a chlorine in the axial position; in fact, in accordance with this,
FeTMPyP4 doesn't unwind closed circular supercoiled DNA.
These pioneering studies stemmed interests in characterizing the porphyrinoid-DNA
interactions, in so far as several factors affect the binding modes. It is clear that the
type of interaction depends on both the structural properties of the porphyrinoid
derivatives and DNA sequences and conformation, however, as well the experimen-
tal conditions, i.e., molar ratio of porphyrin/DNA and ionic strength influence the
binding mode.
Concerning the dependence on ionic strength of the porphyrinoid-DNA
complexes, Pasternack developed a simple theory for the influence of ionic strength
on binding of H
2
TMPyP4 to DNA [
21
]. For the former system the results are typical
of other intercalators, i.e., a plot of log
K
vs log [Na
+
] is linear albeit with a slope
which suggests that the “effective charge” of the porphyrin is closer to two than the
formal charge of + 4. Indeed, when a model of the intercalated porphyrin is
constructed, not all of the
N-
methylpyridyl groups form contacts with phosphate
moieties. Moreover, he demonstrated, by UV and CD experiments on H
2
TMPyP4/
CT-DNA complex at different concentrations of [Na
+
], that porphyrin-base speci-
ficity changes with ionic strength; in particular, porphyrin moves from G-C-rich
regions to AT-rich regions as the ionic strength increases. Finally, he concluded,
unifying notion in his studies and in the previous ones [
22
,
23
], that not only the
avidity but also the nature of polyelectrolyte small molecule interactions may well
be very sensitive to the bulk ionic strength.
The connection among porphyrin binding mode, base pair composition, and
spectroscopic signatures arose out of systematic studies with several porphyrinoid
derivatives and a variety of DNAs, i.e., synthetic polymers as poly(dG-dC) and
poly(dA-dT) or natural mixed sequences of CG and AT.
As mentioned above, extensive evidence demonstrates that H
2
TMPyP4 does
indeed bind intercalatively to double-stranded DNA, unwinding of closed circular
DNA [
13
,
17
,
24
-
27
]. This former and other methods have been employed to
