A theoretical exploration of conformational aspects of ethidium bromide intercalation into a d(CpG)2 minihelix

1H-NMR structural analysis of ethidium bromide complexation with self-complementary deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA) in aqueous solution

Complexation of the trypanocidal drug, ethidium bromide (EB), and the self-complementary deoxytetraribonucleoside triphosphates, 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA), in aqueous salt solution has been investigated using one-dimensional and two-dimensional 500/600 MHz 1H-nmr spectroscopy. Six hundred megahertz two-dimensional homonuclear 1H-nmr spectroscopy (nuclear Overhauser effect spectroscopy) was used for a qualitative determination of the structures of EB binding with the deoxytetranucleotides. Concentration dependencies of proton chemical shifts of the molecules have been measured at constant temperatures (T = 303 or 308 K). Different successive schemes of complex formation between the dye molecule and the tetranucleotides have been examined by taking into account various molecular associations in solution, viz., 1:1, 1:2, 2:1 and 2:2 complexes. Equilibrium reaction constants and the limiting proton chemical shifts in the complexes have been determined. The relative contributions of different types of complexes in the equilibrium mixture have been determined and special features of the dynamic equilibrium have been revealed by analysis of chemical shifts as a function of both the dye and tetranucleotide concentrations. The present analysis leads to the conclusion that EB binds preferentially to the pyrimidine-purine sites of the tetranculeotide duplexes. The results show that the energy of EB binding depends on the base content in the pyrimidine-purine sites of the tetramers and on the nucleotide residuals flanking the preferential site. The most favorable structures of the 1:2 and 2:2 complexes of the dye with the tetranucleotides have been constructed using calculated values of induced chemical shifts of EB protons in conjunction with intermolecular nuclear Overhauser effects. The structures of the EB: tetranucleotide complexes depend on tetramer base sequence and are characterized by differences in helix parameters.

Intercalative binding of ditercalinium to d(CpGpCpG)2: a theoretical study

The structure of the complex formed between ditercalinium, 2,2'-[4,4'-bipiperidine-1,1'-bis-(ethane-1,2-diyl)]bis(10-me thoxy-7H- pyrido[4,3-c]carbazolium) tetramethane sulfonate (NSC 366241), and the self-complementary tetranucleotide duplex d(CpGpCpG)2 has been investigated by means of a novel theoretical approach for modelling the conformational flexibility of nucleic acids. The methodology used is the JUMNA procedure, a molecular mechanics systematics capable of evaluating the internal energy and the interaction energy of a complex formed from a large number of fragments. In the best energy-minimized structures, the piperidinium chains of ditercalinium are located in the major groove of the right-handed oligonucleotide. Calculations show a distortion of the base-paired d(CpGpCpG)2 minihelix consisting of lateral dislocation of one base pair with respect to another along an axis parallel to the long axis; strong propeller twist and tilt of the end base pairs; a collective motion of all base pairs with respect to the helical axis towards the drug; and an overwinding at the exclusion site. The proposed structure of the complex is in good agreement with reported proton NMR data, supporting the feasibility of such model.

A theoretical investigation of the intercalative binding of 7-H pyrido[4.3C]carbazole chromophore into a d(CpG)2 minihelix

Theoretical computations are performed of the intercalative binding to a model d(CpG)2 minihelix of 7-H pyrido[4.3C]carbazole, the precursor of the antitumor bisintercalating drug ditercalinium. The conformations of the intercalation site are generated by the AGNAS procedure (algorithm to generate nucleic acid structures) of Miller and co-workers. The ligand-nucleotide interactions and the nucleotide conformational energies are computed with the SIBFA procedures (sum of interactions between fragments ab initio computed), which use formulas of empirical origin that reproduce ab initio SCF (self-consistent field) computations. Among the candidate intercalation sites most favored energetically, one has a pattern of conformational angles related to the one determined crystallographically by Sobell et al. in a series of x-ray structural studies of small intercalator-dinucleotide monophosphate complexes. Optimal values of the unwinding angle, found in the range of -12 degrees to -14 degrees, are consistent with available experimental data on DNA.

Harmonic dynamics of a DNA hexamer in the absence and presence of the intercalator ethidium

Vibrational normal mode calculations are presented for a DNA hexanucleoside pentaphosphate, d(CpGpCpGpCpG)2, and for its complex with the cationic intercalator ethidium. Two intercalation sites are modeled that differ in DNA backbone torsion angles. Normal mode frequencies for the DNA fragment itself are significantly lower than those reported earlier using different force fields, but an analysis of "effective" frequencies suggests that somewhat higher frequencies are more appropriate. Intercalation leads to significant lowering of mobility for the base pairs adjacent to the drug; in this sequence, the ethidium binding affects the guanosine atoms more strongly than the cytosine atoms. Motions of the bases and the intercalator are analyzed in terms of "twist" about the local helix axis and a "tilt" angle relative to this axis, and the results are compared to fluorescence studies of ethidium-DNA complexes.