1H NMR studies of selective interactions of norfloxacin with double-stranded DNA

Complexation of norfloxacin with DNA in the presence of caffeine

(1)H NMR spectroscopy (500 MHz) has been used to quantify the complexation of the antibacterial antibiotic Norfloxacin (NOR) with DNA in the presence of Caffeine (CAF). Separate studies have been made for the self-association of NOR, its hetero-association with CAF and complexation with a model self-complementary DNA tetramer, 5'-d(TpGpCpA), in order to determine the equilibrium parameters (induced chemical shifts, association constants, enthalpy and entropy) of the two-component mixtures to aid the analysis of the three-component systems. Investigations of the self-association of NOR and its hetero-association with CAF show that the aggregation of NOR molecules and association with CAF in solution are driven by the stacking of aromatic chromophores. The complexation of NOR with d(TGCA) has been analysed in terms of intercalation with the double-stranded form and non-intercalative binding with the single-stranded form of DNA. Investigations of the competitive binding of NOR and CAF with DNA show that at physiological concentrations of NOR (muM) and CAF (mM) the dominant mechanism influencing the affinity of NOR with DNA is the displacement of bound NOR molecules from DNA due to CAF-DNA complexation (i.e. the protector action of Caffeine).

Voltammetry of the interaction of metronidazole with DNA and its analytical applications

Voltammetric methods were used to probe the interaction of antimicrobial drug metronidazole (MTZ) with calf thymus DNA. Binding constants (K) and binding site sizes (s) were determined from the voltammetric data, i.e., shifts in potential and changes in limiting current with the addition of DNA. MTZ showed appreciable electrostatic binding to DNA in solution with K=2.2(+/- 1.3) x 10(4) M(-1) and s=0.34 bp. One reduction peak of MTZ at the bare glassy carbon electrode (GCE) split into two peaks at the DNA modified GCE (DNA/GCE). These changes in the cyclic voltammogram can only be due to the interaction of MTZ with the surface-confined DNA. In addition, the peak current of MTZ at the DNA/GCE was nearly 8-fold of the response at the bare GCE. The low detection limit of 2.0 x 10(-8) M made the DNA/GCE a promising biosensor for MTZ determination. And this method was successfully applied with high precision and accuracy compared with spectroscopic methods (relative error < 6%) for estimation of the total MTZ drug content in pharmaceutical dosage forms.

Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it

Quinolones are antibacterial drugs that are thought to bind preferentially to disturbed regions of DNA. They do not fall into the classical categories of intercalators, groove binders or electrostatic binders to the backbone. We solved the 3D structure of the DNA duplex (ACGCGU-NA)₂, where NA denotes a nalidixic acid residue covalently linked to the 2′-position of 2′-amino-2′-deoxyuridine, by NMR and restrained torsion angle molecular dynamics (MD). In the complex, the quinolones stack on G:C base pairs of the core tetramer and disrupt the terminal A:U base pair. The displaced dA residues can stack on the quinolones, while the uracil rings bind in the minor groove. The duplex-bridging interactions of the drugs and the contacts of the displaced nucleotides explain the high UV-melting temperature for d(ACGCGU-NA)₂ of up to 53°C. Further, non-covalently linked complexes between quinolones and DNA of the sequence ACGCGT can be generated via MD using constraints obtained for d(ACGCGU-NA)₂. This is demonstrated for unconjugated nalidixic acid and its 6-fluoro derivative. The well-ordered and tightly packed structures thus obtained are compatible with a published model for the quinolone–DNA complex in the active site of gyrases.

Voltammetric studies of the interaction of quinacrine with DNA

The binding interaction of the antimalarial drug quinacrine with herring sperm deoxyribonucleic acid (DNA) has been studied by square wave voltammetry. The binding parameters, the binding constant K and the binding site size s, were obtained simultaneously by the analysis of bound and free quinacrine concentration corresponding to the limits of slow and fast binding kinetics compared to the experimental timescale. The binding constant and the binding site size for the interaction of quinacrine with DNA were K = 1.59 (+/-0.18)x10(5) M(-1) and s = 7.1 (+/-0.15) base pairs and K = 7.35 (+/-0.83)x10(5) M(-1), s = 6.2 (+/-0.02) base pairs for the limiting conditions of static and mobile binding equilibrium respectively. The standard Gibbs free energy change (Delta G0 = - RT ln K) is approximately -29.67 kJ/mol at 25 degrees C, which highlights the spontaneity of the binding of quinacrine with DNA. The binding of quinacrine to herring sperm DNA results in peak potential shifts in voltammetric and a red shift in UV-absorption measurements. The ionic strength dependence of the binding constant is not large. Furthermore, the relative viscosity of DNA increases in the presence of quinacrine. These characteristics strongly support the intercalation of quinacrine into DNA. The results also show that the intercalation of quinacrine into DNA may occur at approximately every seventh base pair.