A theoretical study of the interaction of 4′,6 diamidino-2-phenylindole (DAPI) with the double-stranded oligonucleotides (dA-dT)11 and (dA)11·(dT)11

A study of the interaction of DAPI with DNA containing AT and non-AT sequences--molecular specificity of minor groove binding drugs

The binding specificity of DAPI to DNA has been probed by analysing its interactions with DNA octamers consisting of different base sequences, which include adenine, guanine, 2-amino adenine and inosine, using molecular mechanics methods. Presence of AT and non-AT base pairs in the immediate vicinity of the binding site, containing AT and non-AT base pairs is also investigated. Results show that DAPI most prefers to bind to homopolymer of AT, and least to the duplex containing alternating GC bases. DAPI interacts with homopolymeric duplexes in two possible orientations related by 180 degrees with nearly same affinity. Affinity of DAPI towards DNA comprising the modified bases, inosine and 2-amino adenine, is in between these extremities. The binding affinity is reduced to some extent by the occurrence of non AT bases flanking the four base paired binding region. An interesting revelation is that one can visualise DAPI to form a hydrogen bond with O2 of cytosine indicating that the 2-amino group of purines does not per se sterically preclude DAPI from residing in the minor groove of B-DNA helix. On the other hand, repulsive nature of electrostatic interactions that prevail at the minor groove consequent to the presence of these sequences contribute decisively in preventing further diffusion of the drug. Thus, electrostatics, rather than hydrogen bonding to bases, seemingly play an important role in determining the specificity of interaction. The retention of drug binders in the minor groove and therefore recognition, is governed by the combined effect of these various forces.

Investigations on mutagenicity and genotoxicity of pentamidine and some related trypanocidal diamidines

Pentamidine, DAPI and some related compounds (DAI, 6-Br-AI, DPTN, DIPI, 3-Am-DAI, DiaPBF) were investigated in 2 different screening test systems for their potential mutagenic and cytotoxic effects, in the light of their binding to DNA. In the Ames test using Salmonella typhimurium strains TA98 and TA100 with and without metabolic activation no mutagenic effects could be observed. All diamidines tested, except DAI, were toxic at concentrations of 0.5 and 1.0 mumole/plate. In the sister-chromatid exchange (SCE) assay with human peripheral lymphocytes all compounds tested were growth-retarding particularly in the G0 phase. A significant induction of SCEs could only be seen after treatment with the monoamidino compound 6-Br-AI at a concentration of 100 mumole/l. It is concluded from the data obtained that pentamidine and related diamidines in the 2 assays tested show no mutagenic or genotoxic effects, in spite of their tight binding to DNA.

Time-resolved fluorescence of DAPI in solution and bound to polydeoxynucleotides

Fluorescence decay studies, obtained by multifrequency phase-modulation fluorometry, have been performed on DAPI in solution and complexed with natural and synthetic polydeoxynucleotides. DAPI decay at pH 7 was decomposed using two exponential components of 2.8 and 0.2 ns of lifetime values, respectively. The double exponential character of the decay was maintained over a large pH range. Phase- and modulation-resolved spectra, collected between 420 and 550 nm, have indicated at least two spectral components associated with the two lifetime values. This, plus the observation of the dependence of the emission spectrum on the excitation wavelength, suggests a lifetime heterogeneity originating from ground-state molecular conformers, partially affected by pH changes. DAPI complexed with natural polydeoxynucleotides retained most of the features of DAPI decay in solution, except for the value of the long lifetime component that was longer (approximately 4 ns) and the relative fractional fluorescence intensities of the two components that were inverted. AT polymers/DAPI complexes show single exponential decay. Solvent shielding when DAPI is bound to DNA changes the indole ring solvation and stabilizes the longer lifetime decay component. For poly(GC)/DAPI complex, the decay was similar to that of free DAPI in solution, proving the dependence on the polydeoxynucleotides sequence the different types of binding and the reliability of the fluorescence method to solve them.

The structure of DAPI bound to DNA

The structure of the DNA fluorochrome 4'-6-diamidine-2-phenyl indole (DAPI) bound to the synthetic B-DNA oligonucleotide C-G-C-G-A-A-T-T-C-G-C-G has been solved by single crystal x-ray diffraction methods, at a resolution of 2.4 A. The structure is nearly isomorphous with that of the native DNA molecule alone. With one DAPI and 25 waters per DNA double helix, the residual error is 21.5% for the 2428 reflections above the 2-sigma level. DAPI inserts itself edgewise into the narrow minor groove, displacing the ordered spine of hydration. DAPI and a single water molecule together span the four AT base pairs at the center of the duplex. The indole nitrogen forms a bifurcated hydrogen bond with the thymine O2 atoms of the two central base pairs, as with netropsin and Hoechst 33258. The preference of all three of these drugs for AT regions of B-DNA is a consequence of three factors: (1) The intrinsically narrower minor groove in AT regions than in GC regions of B-DNA, leading to a snug fit of the flat aromatic drug rings between the walls of the groove. (2) The more negative electrostatic potential within the minor groove in AT regions, attributable in part to the absence of electropositive-NH2 groups along the floor of the groove, and (3) The steric advantage of the absence of those same guanine-NH2 groups, thus permitting the drug molecule to sink deeper into the groove. Groove width and electrostatic factors are regional, and define the relative receptiveness of a section of DNA since they operate over several contiguous base pairs. The steric factor is local, varying from one base pair to the next, and hence is the means of fine-tuning sequence specificity.