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The characterization of the binding interaction
between DNA and small molecules has always
been a point of interest and extensively researched over the years. The prime
interest in these studies mainly lies in the fact that the DNA-binder agents are
supposed to have the potential to act as drugs.

 The present
experimental study attempts to investigate the binding interaction between two
types of acridone derivative, 8-choloro acridone
(CA) and nitrile cyanide acridone (NCA), and calf thymus DNA (ctDNA). To perform
this study, several spectroscopic
techniques were employed. The obtained result revealed that CA and NCA can bind
to ctDNA by a quenching constant of 2.949×103 and 7.063×103
M-1 respectively.
Further analysis pointed out that the interaction between CA and ctDNA was
controlled by a dynamic quenching mechanism while the dominant quenching
process in ctDNA-NCA interaction was
static. Calculating and analyzing the thermodynamic parameters allows an
estimation of the forces that drives the complex formation. In present study, the
thermodynamic properties of the binding
process indicated that the resulting ctDNA-CA and ctDNA-NCA
complexes were stabilized by hydrophobic and van der Waals intercations
respectively. The fluorescence
displacement experiments were conducted by using ethidium bromide (EB) and
acridone orang (AO) as fluorescence probes and showed that CA and NCA compete
against intercalator probes and thereby they probably interact with ctDNA
through intercalation. Given that the melting temperature of
ctDNA went up by 6-8 C in the presence of CA and NCA, it can be thus inferred
that these two compound probably intercalated into ctDNA and brought greater
stability in ctDNA. A closer insight into the modes of binding was achieved by measuring and comparing ctDNA
viscosity in the absence and presence of CA and NCA. The results displayed that
the presence of CA resulted in a decrease in the relative viscosity of ctDNA
which is a characteristic of non-classical intercalation bindings. In contrast,
the ctDNA relative viscosity increased through binding on NCA which reflect the
fact that NCA bound ctDNA intercalately. The effect of ionic strength on the interactions indicated that the
ctDNA-NCA and ctDNA-CA interactions were relatively dependent and independent
on the salt concentration respectively. These
findings allowed us to deduce that electrostatic interactions moderately
contributed in the interaction between ctDNA and NCA. However, these external binding
interactions are much weaker than intercalation. The CD spectra of ctDNA
were collected in the presence and absence of CA and NCA. The minor induced conformational
changes in ctDNA through the interactions with CA and NCA were reflected in the
gentle changes of ctDNA spectra upon incremental addition of CA and NCA.
Moreover, it was shown that CA has higher affinity to ss ctDNA whereas NCA tends to bind native ctDNA more strongly. All things considered,
our investigation and results implied that CA and NCA interacted with ctDNA via
intercalation mode. Moreover, the interaction between NCA and ctDNA is much
stronger compared to the ctDNA-CA binding interaction.

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